(/) [Biocaml_internal_pervasives.Filename.Infix] | p1/p2 is equivalent to concat p1 p2 .
|
(>>=) [Biocaml_entrez.Fetch] | |
(>|=) [Biocaml_entrez.Fetch] | |
(|?) [Biocaml_internal_pervasives] | |
A | |
accuracy [Biocaml_roc] | |
add [Biocaml_iset] |
Add the given int to the set, returning a new set
|
add [Biocaml_interval_tree] | add lo hi v t adds the interval (lo , hi ) labeled with value
v to the contents of t .
|
add [Biocaml_genomeMap.LMap_spec] | |
add [Biocaml_accu.Relation] | |
add [Biocaml_accu.Counter] | |
add [Biocaml_accu] | add accu x y updates the value in accu for
the bin of x by an increment y
|
add_child [Biocaml_msg.Tree] | add_child t x inserts x as the right-most child of t .
|
add_extensions [Biocaml_tags] |
For a given
tags value and a list of file-base-names add
extensions to the files, and return also the base-names not touched.
|
add_range [Biocaml_iset] | add_range t lo hi adds the range of integers lo, hi (including both endpoints) to
the given set, returning a new set
|
after [Biocaml_iset] | after ~n t returns the portion of t in the range n+1, max_int
|
after [Biocaml_range] | after u v is equivalent to before v u .
|
alg_name [Biocaml_bar] |
Name of algorithm used to generate scores.
|
alg_version [Biocaml_bar] |
Version number of algorithm used.
|
alignment_of_sexp [Biocaml_sam] | |
all_positional [Biocaml_range] |
Return true if all pairs of given ranges are positionally comparable.
|
any_overlap [Biocaml_range] |
Return true if any pair of given ranges overlap each other.
|
auc [Biocaml_roc] | auc e computes the area above the X-axis and under the piecewise linear curve
passing through the points in e .
|
B | |
background_of_sequence [Biocaml_pwm] | background_of_sequence seq pc estimates the base
frequency in seq using pc as pseudo-counts.
|
bed_graph_value_of_sexp [Biocaml_wig] | |
bed_to_string [Biocaml_track.Transform] |
Create a printer for track files containing Bed(Graph) lines.
|
before [Biocaml_iset] | before x t returns the portion of t in the range min_int, n-1
|
before [Biocaml_range] | before u v is true if strict_before u v || equal u v .
|
best_hit [Biocaml_pwm] | best_hit mat seq returns the position and score of the best
alignment found in seq for the motif mat .
|
bin [Biocaml_histogram] | bin hist i returns the i th bin of hist .
|
bin_exn [Biocaml_histogram] | bin hist i returns the i th bin of hist .
|
bug [Biocaml_msg] |
Create a string communicating an error, warning, or bug.
|
C | |
cardinal [Biocaml_iset] |
Returns the number of elements in the set
|
cardinal [Biocaml_interval_tree] | |
char_seq_item_to_raw_item [Biocaml_fasta.Transform] |
Cut a stream of
char_seq item s into a stream of char_seq
raw_item s, where lines are cut at items_per_line
characters (where items_per_line is defined with the
`max_items_per_line _ tag, if not specified the default is
80).
|
char_seq_of_sexp [Biocaml_fasta] | |
char_seq_raw_item_to_item [Biocaml_fasta.Transform] |
Aggregate a stream of FASTA
char_seq raw_item s into char_seq
item s.
|
char_seq_raw_item_to_string [Biocaml_fasta.Transform] |
Print
char_seq item s.
|
char_seq_raw_item_to_string [Biocaml_fasta] |
Convert a
raw_item to a string (ignore comments).
|
char_sequence_default [Biocaml_fasta.Tags] |
The default tags (for
char_seq ).
|
check_integrity [Biocaml_interval_tree] |
Used for debugging purpose, should be removed in the long run
|
choose [Biocaml_iset] |
Returns some element in the set
|
cigar_op_of_sexp [Biocaml_sam] | |
closest [Biocaml_genomeMap.LMap] | closest loc lmap returns the location in lmap that is the
closest to loc , along with its annotation and the actual (minimal)
distance.
|
closest [Biocaml_genomeMap.LSet] | closest loc lset returns the location in lset that is the
closest to loc , along with the actual (minimal)
distance.
|
cnd [Biocaml_math] |
Cumulative distribution function.
|
col_exn [Biocaml_pos] |
Return the file name, line number, or column number.
|
col_names [Biocaml_bpmap] |
Names of columns in BPMAP file, in the order required by specification.
|
column [Biocaml_math] | column m i extracts the i th column of matrix m .
|
comment_of_sexp [Biocaml_wig] | |
compare [Biocaml_iset] |
Compare two sets.
|
compare [Biocaml_strandName] | |
compare_containment [Biocaml_range] | compare_containment u v returns -1 if u is a strict subset of v , 0 if u is equal to v , +1 if u is a strict superset of v , and returns None otherwise.
|
compare_hi [Biocaml_range] |
Compare by ranges'
hi bounds, ignoring lo bounds.
|
compare_lo [Biocaml_range] |
Compare by ranges'
lo bounds, ignoring hi bounds.
|
compare_lo_then_hi [Biocaml_range] |
Return order between
lo bounds unless they are equal, in which case return order between hi bounds.
|
compare_positional [Biocaml_range] | compare_positional u v returns -1 if u is strictly before v , 0 if u is equal to v , +1 if u is strictly after v , and returns None otherwise.
|
compl [Biocaml_iset] |
Create the complement of the given set - i.e.
|
compose [Biocaml_internal_pervasives.Order] | |
compose [Biocaml_transform] | compose t u composes t and u .
|
compose_result_left [Biocaml_transform] |
Like
Biocaml_transform.compose_results but only the first transform returns
Result.t s.
|
compose_results [Biocaml_transform] | |
compose_results_merge_error [Biocaml_transform] |
Like
Biocaml_transform.compose_results but with a pre-specified on_error
function.
|
contents [Biocaml_lines.Buffer] |
Return any remaining lines and the unfinished string, without
removing them from the buffer.
|
coord_convention [Biocaml_bar] |
Probe coordinate convention used.
|
copy [Biocaml_histogram] |
Copy histogram.
|
count [Biocaml_histogram] | count hist i returns the count the i th bin.
|
count_exn [Biocaml_histogram] | count hist i returns the count the i th bin.
|
counts [Biocaml_accu] | |
create [Biocaml_accu.Relation] | |
create [Biocaml_accu.Counter] | |
create [Biocaml_accu] | create ~n e f op creates an accumulator, which maps instances to bins
with f , uses e as a neutral element (that is the value associated to a
bin before any value has been added to it) and updates the value of a bin
with op .
|
current_position [Biocaml_lines.Buffer] |
Get the current position in the stream.
|
D | |
data [Biocaml_cel] | data bpmap cels returns a list associating probes with pairs of
(PM,MM) idata in each of the given cel files (in the same order of
course).
|
data_type [Biocaml_bar] |
Return the type of data, either "signal" or "p-value".
|
default [Biocaml_wig.Tags] |
Default tags (
{allow_empty_lines = false; sharp_comments = true} ).
|
default [Biocaml_table.Row.Tags] |
The default tags define a loose TSV format.
|
default [Biocaml_gff.Tags] |
Default tags for a random Gff file:
{version = `three; allow_empty_lines = false; sharp_comments = true} .
|
default_extension [Biocaml_tags] |
Get a filename extension for a given
format.
|
default_extension [Biocaml_table.Row.Tags] |
Give a file extension (
"tsv" , "csv" , or "table" ).
|
default_extensions [Biocaml_tags] |
Do like
default_extension but for potentially multiple file-formats.
|
diff [Biocaml_iset] |
Compute the difference between two sets.
|
diff [Biocaml_rSet] |
Set difference.
|
diff [Biocaml_genomeMap.Selection] | |
disable [Biocaml_internal_pervasives.Debug] | |
E | |
each_segment_properly_aligned [Biocaml_sam.Flags] | |
efetch_url [Biocaml_entrez] |
Construction of efetch URLs.
|
elements [Biocaml_iset] |
Returns a list of all elements in the set
|
elements [Biocaml_interval_tree] | |
empty [Biocaml_iset] |
The empty set
|
empty [Biocaml_rSet] |
The empty set.
|
empty [Biocaml_lines.Buffer] |
Empty the buffer.
|
empty [Biocaml_interval_tree] |
the empty tree
|
enable [Biocaml_internal_pervasives.Debug] | |
epsilon [Biocaml_math] | epsilon f init fin applies f n fin to all numbers from init to fin and adds them up.
|
equal [Biocaml_iset] |
Test whether two sets are equal.
|
equal [Biocaml_strandName] | |
err [Biocaml_msg] | |
escapable_string [Biocaml_internal_pervasives.Parse] |
Parse a string potentially escaped with OCaml string
conventions, or stop at
stop_before character if it is not
escaped.
|
escape [Biocaml_internal_pervasives.Url] |
Convert non-alphanumeric characters to their
"%HX"
URL-escaping format.
|
esearch_answer_of_string [Biocaml_entrez] |
Parses an answer of esearch under XML format
|
esearch_url [Biocaml_entrez] |
Construction of esearch URLs.
|
esummary_url [Biocaml_entrez] |
Construction of esummary URLs
|
eval [Biocaml_genomeMap.Signal] |
function evaluation at some point in the genome
|
even [Biocaml_math] |
True if given integer is even.
|
exists [Biocaml_iset] |
Test whether some element of a set satisfies a predicate
|
expand_assoc_list [Biocaml_range] | exp_assoc_list dat returns a list associating each integer i with the list of values associated with all ranges overlapping i in dat .
|
expand_header_line [Biocaml_sam] |
Parse a header line into a more detailed type.
|
F | |
f [Biocaml_pos] | |
f1_score [Biocaml_roc] | |
factorial [Biocaml_math] |
Self-explanatory.
|
false_discovery_rate [Biocaml_roc] | |
false_positive_rate [Biocaml_roc] | |
fast_scan [Biocaml_pwm] |
Identical to
scan but directly implemented in C
|
fasta_pair_to_fastq [Biocaml_fastq.Transform] |
Create a transform that builds
item records thanks
to sequences from Fasta.(char_seq item) values
and qualities converted from
Fasta.(int_seq item) values.
|
fastq_to_fasta_pair [Biocaml_fastq.Transform] |
Create a transform that split a FASTQ item into to FASTA items
(i.e.
|
feed [Biocaml_transform] | feed t i stores i into the buffered transform.
|
feed_line [Biocaml_lines.Buffer] |
Feed the parser with a line.
|
feed_string [Biocaml_lines.Buffer] |
Feed the parser with an arbitrary string buffer.
|
fetch [Biocaml_entrez.Fetch] | |
file_exn [Biocaml_pos] | |
file_format_of_sexp [Biocaml_tags] | |
filter [Biocaml_iset] |
Builds the subset of those elements that satisfy the predicate
|
filter_compose [Biocaml_transform] | filter_compose t u ~destruct ~reconstruct produces a transform
that feeds a filtered subset of t s outputs to u .
|
filter_overlapping [Biocaml_interval_tree] |
Create an interval tree with the elements which overlap with
[low, high] .
|
find_bin_index [Biocaml_histogram] | find_bin_index hist x returns the index of the bin in hist
containing x .
|
find_closest [Biocaml_interval_tree] | find_closest lo hi t returns the interval in t which is at
minimal distance of the interval [lo ;hi ].
|
find_intersecting_elem [Biocaml_interval_tree] | find_intersecting_elem a b t is equivalent to Stream.filter ~f:(fun
(x,y,_) -> intersects x y t) (stream t) but is more efficient.
|
find_min_range [Biocaml_range] | find_min_range v pred i finds the minimum sized range within v centered around i that satisfies pred .
|
find_min_window [Biocaml_math] | find_min_window a pred i finds the minimum sized window within a centered around index i that satisfies pred .
|
find_regions [Biocaml_range] |
TO DO: fill in this documentation.
|
find_regions [Biocaml_math] | find_regions ~max_gap pred a returns an array of (first,last) index pairs denoting boundaries (inclusive) of regions found in a .
|
first_segment [Biocaml_sam.Flags] | |
fixed_step_of_sexp [Biocaml_wig] | |
fl [Biocaml_pos] | |
flat_background [Biocaml_pwm] |
Uniform distribution over A, C, G, T
|
flc [Biocaml_pos] |
Methods for creating a position.
|
fold [Biocaml_iset] | fold f t x0 returns the final result of merging each element of
t into x0 using merge function f
|
fold [Biocaml_genomeMap.LMap_spec] |
fold guaranteed on increasing order keywise, and for each key
|
fold [Biocaml_genomeMap.Signal] |
folds on constant intervals of the function, in increasing order
|
fold [Biocaml_bpmap] | |
fold_left [Biocaml_seq] |
see String.fold_left.
|
fold_lefti [Biocaml_seq] |
String.fold_lefti
|
fold_range [Biocaml_iset] |
As fold, but operates on contiguous ranges
|
for_all [Biocaml_iset] |
Tests whether a predicate applies to all elements of the set
|
for_all [Biocaml_line] | |
format [Biocaml_table.Row.Tags] |
Get the defined format if any.
|
from [Biocaml_iset] | from ~n t returns the portion of t in the range n, max_int
|
from_tags [Biocaml_tags.Input_transform] |
Create an
Input_transform.t from tags describing the format.
|
from_tags [Biocaml_tags.Output_transform] |
Guess the
Output_transform.t from file tags.
|
G | |
gap [Biocaml_range] | gap u v returns the size of the gap between u and v .
|
genomic_map [Biocaml_bar] |
File path of bpmap file used to generate scores.
|
get [Biocaml_accu] | get accu x returns the value associated to b in accu .
|
get_tags [Biocaml_fasta.Random] |
Get the first
Tags.t in the specification, if any.
|
gff_to_string [Biocaml_track.Transform] |
Create a printer for track files containing GFF lines.
|
group2 [Biocaml_lines.Transform] |
Return a transform that converts a stream of lines to a stream
of pairs of lines.
|
guess_from_filename [Biocaml_tags] |
Get a tag as precise as possible for a given filename.
|
H | |
has_multiple_segments [Biocaml_sam.Flags] | |
histogram [Biocaml_math] |
Return histogram of values using
cmp (default = Pervasives.compare ) for comparison.
|
I | |
identity [Biocaml_transform] | identity () returns a transform that simply returns its inputs
as outputs without modification (it can be seen as a
simple Queue.t ).
|
idxsort [Biocaml_math] | idxsort cmp a is like Array.sort but a is unaltered, and instead an array of the indices in sorted order is returned.
|
ifold [Biocaml_cel] | ifold f a t folds over data rows in intensity section of t .
|
iiter [Biocaml_cel] | iiter f t iterates over the rows in intensity section of t .
|
in_channel_strings_to_stream [Biocaml_transform] | in_channel_strings_to_stream ic t returns a stream of 'output s
given a transform t that knows how to produce 'output s from
strings.
|
in_channel_to_bed_graph [Biocaml_wig] |
Get a stream of
bed_graph_value values out of a WIG-file input-channel.
|
in_channel_to_bed_graph_exn [Biocaml_wig] |
Do like
in_channel_to_bed_graph but each call to Stream.next
may throw an exception.
|
in_channel_to_char_seq_item_stream [Biocaml_fasta] |
Parse an input-channel into a stream of
char_seq item results.
|
in_channel_to_char_seq_item_stream_exn [Biocaml_fasta] |
Returns a stream of
char_seq item s.
|
in_channel_to_char_seq_raw_item_stream [Biocaml_fasta] |
Parse an input-channel into a stream of
char_seq raw_item results.
|
in_channel_to_char_seq_raw_item_stream_exn [Biocaml_fasta] |
Returns a stream of
char_seq raw_item s.
|
in_channel_to_int_seq_item_stream [Biocaml_fasta] |
Parse an input-channel into a stream of
int_seq item results.
|
in_channel_to_int_seq_item_stream_exn [Biocaml_fasta] |
Returns a stream of
int_seq item s.
|
in_channel_to_int_seq_raw_item_stream [Biocaml_fasta] |
Parse an input-channel into a stream of
int_seq raw_item results.
|
in_channel_to_int_seq_raw_item_stream_exn [Biocaml_fasta] |
Returns a stream of
int_seq raw_item s.
|
in_channel_to_item_stream [Biocaml_wig] |
Get a stream of
item values out of an input-channel.
|
in_channel_to_item_stream [Biocaml_sam] |
Parse an input-channel into a stream of high-level items.
|
in_channel_to_item_stream [Biocaml_psl] | |
in_channel_to_item_stream [Biocaml_gff] |
Parse an input-channel into
item values.
|
in_channel_to_item_stream [Biocaml_fastq] |
Parse an input-channel into a stream of
item results.
|
in_channel_to_item_stream [Biocaml_bed] |
Parse an input-channel into
item values.
|
in_channel_to_item_stream [Biocaml_bam] |
Create a stream of full
Sam.item results from an input-channel.
|
in_channel_to_item_stream_exn [Biocaml_wig] |
Do like
in_channel_to_item_stream but each call to Stream.next
may throw an exception.
|
in_channel_to_item_stream_exn [Biocaml_sam] |
Like in_channel_to_item_stream but each call to
Stream.next may
raise Error _
|
in_channel_to_item_stream_exn [Biocaml_psl] | |
in_channel_to_item_stream_exn [Biocaml_gff] |
Like
in_channel_to_item_stream but use exceptions for errors
(raised within Stream.next ).
|
in_channel_to_item_stream_exn [Biocaml_fastq] |
Returns a stream of
item s.
|
in_channel_to_item_stream_exn [Biocaml_bed] |
Like
in_channel_to_item_stream but use exceptions for errors
(raised within Stream.next ).
|
in_channel_to_item_stream_exn [Biocaml_bam] |
Create a stream of
Sam.item s from an input-channel (any call to
Stream.next may throw an Error _ exception).
|
in_channel_to_raw_item_stream [Biocaml_sam] |
Parse an input-channel into a stream of low-level (“raw”) items.
|
in_channel_to_raw_item_stream [Biocaml_bam] |
Create a stream of raw_item results from an input-channel.
|
in_channel_to_raw_item_stream_exn [Biocaml_sam] |
Like in_channel_to_raw_item_stream but each call to
Stream.next may
raise Error _
|
in_channel_to_raw_item_stream_exn [Biocaml_bam] |
Create a stream of raw_items from an input-channel (any call to
Stream.next may throw an Error _ exception).
|
in_range [Biocaml_histogram] | in_range hist x is true if x greater than or equal to minimum
hist and strictly less than maximum hist .
|
in_sbml [Biocaml_sbml] |
Returns an sb_model read from input stream
|
increment [Biocaml_histogram] | increment delt hist x increments the count of the bin containing
x by delt (default is 1.0).
|
incrl [Biocaml_pos] | incrl pos k increments the line number of pos by k .
|
int_seq_item_to_raw_item [Biocaml_fasta.Transform] |
Cut a stream of
int_seq item s into a stream of int_seq
raw_item s, the default line-cutting threshold is 27
(c.f.
|
int_seq_of_sexp [Biocaml_fasta] | |
int_seq_raw_item_to_item [Biocaml_fasta.Transform] |
Aggregate a stream of FASTA
int_seq raw_item s into int_seq
item s.
|
int_seq_raw_item_to_string [Biocaml_fasta.Transform] |
Print
int_seq item s.
|
int_seq_raw_item_to_string [Biocaml_fasta] |
Convert a
raw_item to a string (ignore comments).
|
int_sequence_default [Biocaml_fasta.Tags] |
The default tags (for
int_seq ).
|
inter [Biocaml_iset] |
Compute the intersection of two sets.
|
inter [Biocaml_rSet] |
Set intersection.
|
inter [Biocaml_genomeMap.Selection] | |
intersect [Biocaml_range] | intersect u v returns the range representing the intersection of u and v .
|
intersecting_elems [Biocaml_genomeMap.LMap] | intersecting_elems loc lmap returns an enumeration of elements
in lmap whose location intersects with loc .
|
intersecting_elems [Biocaml_genomeMap.LSet] | intersecting_elems loc lset returns an enumeration of all
locations in lset that intersect loc .
|
intersection_size [Biocaml_genomeMap.Selection] | |
intersects [Biocaml_interval_tree] | intersects a b t returns true if one interval in t
intersects with the interval [a ;b ].
|
intersects [Biocaml_genomeMap.LMap_spec] | |
intersects [Biocaml_genomeMap.LMap] | intersects loc lmap returns true if loc has a non-empty
intersection with one of the locations in lmap , and returns
false otherwise
|
intersects [Biocaml_genomeMap.LSet] | intersects loc lmap returns true if loc has a non-empty
intersection with one of the locations in lmap , and returns
false otherwise
|
intersects [Biocaml_genomeMap.Selection] | intersects loc sel returns true if loc has a non-empty
intersection with sel , and false otherwise.
|
intersects_range [Biocaml_iset] | |
is_char_sequence [Biocaml_fasta.Tags] |
Test the value of
t.sequence .
|
is_empty [Biocaml_iset] |
Test whether a set is empty, returns
true if the set is empty.
|
is_empty [Biocaml_rSet] |
Return true if given set is empty.
|
is_empty [Biocaml_lines.Buffer] |
Tell if the parser's buffers are empty or not.
|
is_empty [Biocaml_interval_tree] | |
is_int_sequence [Biocaml_fasta.Tags] |
Test the value of
t.sequence .
|
is_nucleic_acid [Biocaml_seq] |
True if given character represents one of the allowed nucleic acid
codes, case-insensitive.
|
item_of_line [Biocaml_bed] |
Basic parsing of a single line.
|
item_of_sexp [Biocaml_wig] | |
item_of_sexp [Biocaml_table.Row] | |
item_of_sexp [Biocaml_sam] | |
item_of_sexp [Biocaml_psl] | |
item_of_sexp [Biocaml_lines] | |
item_of_sexp [Biocaml_gff] | |
item_of_sexp [Biocaml_fastq] | |
item_of_sexp [Biocaml_fasta] | |
item_of_sexp [Biocaml_bed] | |
item_to_bed_graph [Biocaml_wig.Transform] |
Create a transform which converts
`variable_step_value _ and
`fixed_step_value _ values to `bed_graph_value _ values, using the
current state.
|
item_to_line [Biocaml_table.Row.Transform] |
Create a
Biocaml_transform.t that converts rows to lines
using the first separator in the tags or '\t' if none
(default tags : Biocaml_table.Row.Tags.default ).
|
item_to_line [Biocaml_bed] |
Basic “printing” of one single
item .
|
item_to_raw [Biocaml_sam.Transform] |
Create a transform that downgrades
item s to raw_item s
|
item_to_raw [Biocaml_bam.Transform] |
Create a transform that downgrades
Sam.item s to raw_item s.
|
item_to_raw_of_sexp [Biocaml_sam.Error] | |
item_to_raw_of_sexp [Biocaml_bam.Error] | |
item_to_string [Biocaml_wig.Transform] |
Create the transform that prints
item values to strings.
|
item_to_string [Biocaml_wig] |
Convert an
item to a string (including new line characters).
|
item_to_string [Biocaml_lines.Transform] |
Return a transform that output
Line.item s to strings (in other
words a buffer with the lines plus their end-of-line
character).
|
item_to_string [Biocaml_gff.Transform] |
Create a printer for a given version.
|
item_to_string [Biocaml_gff] |
Convert an item to a string.
|
item_to_string [Biocaml_fastq.Transform] |
Create a
Biocaml_transform.t from item values to strings.
|
item_to_string [Biocaml_fastq] |
Convert a
item to a string.
|
item_to_string [Biocaml_bed.Transform] |
Create a
Biocaml_transform.t which “prints” BED data
(reminder: includes ends-of-line).
|
item_type_of_sexp [Biocaml_table.Row] | |
iter [Biocaml_iset] | iter f t calls f once for each element of t
|
iter [Biocaml_bpmap] | |
iter_range [Biocaml_iset] | iter_range ~f t calls f once for each contiguous range of t .
|
L | |
l [Biocaml_pos] | |
last_segment [Biocaml_sam.Flags] | |
lc [Biocaml_pos] | |
leaf [Biocaml_msg.Tree] | |
length [Biocaml_seq] |
Length of sequence.
|
level [Biocaml_zip.Default] |
The default compression level used in
Transform.zip .
|
line_exn [Biocaml_pos] | |
line_parsing_of_sexp [Biocaml_table.Row.Error] | |
line_to_item [Biocaml_table.Row.Transform] |
Create a
Biocaml_transform.t that converts lines to
table-rows according to the tags (default: Biocaml_table.Row.Tags.default ).
|
line_to_item [Biocaml_psl] | |
load [Biocaml_jaspar] |
Load a
motif list from a given path (reading file path ^
"/matrix_list.txt" ).
|
log [Biocaml_math] |
Logarithm.
|
log10 [Biocaml_math] |
Base 10 logarithm.
|
log2 [Biocaml_math] |
Base 2 logarithm.
|
lstrip [Biocaml_line] | |
ltqnorm [Biocaml_math] |
Lower tail quantile for standard normal distribution function.
|
M | |
mad [Biocaml_math] |
Median absolute deviation (MAD).
|
make [Biocaml_internal_pervasives.Debug] | |
make [Biocaml_transform] | make ~feed ~next () creates a transform that can be
fed with feed and read from with next .
|
make [Biocaml_roc] |
Given an enum
pos (resp.
|
make [Biocaml_range] | make l u returns the range from l to u .
|
make [Biocaml_pwm] |
Builds a PWM from a count_matrix and a background
|
make [Biocaml_pos] | |
make [Biocaml_lines.Transform] |
Build a stoppable line-oriented parsing_buffer.
|
make [Biocaml_lines.Buffer] |
Make a new empty buffer.
|
make [Biocaml_histogram] | make cmp bins returns a new histogram from the given bins ,
all initialized to a count of 0.0.
|
make [Biocaml_genomeMap.LMap_spec] | |
make [Biocaml_genomeMap.Signal] | |
make_general [Biocaml_transform] |
The most general way to make a transform.
|
make_merge_error [Biocaml_lines.Transform] |
Do like
make but merge `incomplete_input _ with the
errors of ~next (which must be polymorphic variants).
|
make_opt [Biocaml_range] |
Like
make but returns None instead of raising exception.
|
make_result [Biocaml_transform] |
Like
Biocaml_transform.make but the output is a Result.t .
|
make_uniform [Biocaml_histogram] | make_uniform min max n returns a histogram with n bins
uniformly dividing up the range from min to max .
|
mass [Biocaml_mzData.Precursor] | mass p return the mass of the precursor p without charge.
|
math_to_string [Biocaml_sbml] |
Returns a string with sb_math converted into a S-expression
|
max [Biocaml_math] |
Return maximum value in given array.
|
max_array_length_error [Biocaml_msg] |
String explaining OCaml's array length limitation on 32-bit machines.
|
max_elt [Biocaml_iset] |
Returns the maximum element in the set
|
max_gap_of_positional [Biocaml_range] |
Return maximum gap between adjacent pairs of given ranges.
|
maximum [Biocaml_histogram] |
Upper limit of the maximum bin.
|
mean [Biocaml_math] |
Mean.
|
median [Biocaml_math] |
Median.
|
mem [Biocaml_iset] |
test whether a given int is a member of the set
|
member [Biocaml_range] | member t k returns true if t contains k .
|
min [Biocaml_math] |
Return minimum value in given array.
|
min_elt [Biocaml_iset] |
Returns the minimum element in the set
|
minimum [Biocaml_histogram] |
Lower limit of the minimum bin.
|
minus_plus [Biocaml_strandName] |
Return "-" or "+".
|
mix [Biocaml_transform] | mix t u returns a transform that takes as input a pair of the
inputs expected by t and u , and outputs
either both outputs, or, when one transform has reach the end of
its stream, the output of the remaining one (as `left _ or
`right _ ).
|
mm [Biocaml_cel] |
Similar to
Biocaml_cel.data but the data returned are the MM mean intensity
values in cels .
|
N | |
name [Biocaml_transform] | name t returns the name of t .
|
name [Biocaml_tags.Input_transform] |
Get a string describing and input transform (for debug/display
purposes).
|
name [Biocaml_tags.Output_transform] |
Get a string naming the transform (for debug/error messages).
|
negative_predictive_value [Biocaml_roc] | |
next [Biocaml_transform] | next t returns an output value if possible, `not_ready if t
needs to be fed with more input before it can produce an output,
or `end_of_stream if t has been stopped and has no more
data.
|
next_line [Biocaml_lines.Buffer] |
Get the next line.
|
next_line_exn [Biocaml_lines.Buffer] |
Get the next line, but throw
No_next_line if there is no line
to return.
|
next_segment_unmapped [Biocaml_sam.Flags] | |
next_seq_is_reverse_complemented [Biocaml_sam.Flags] | |
not_passing_quality_controls [Biocaml_sam.Flags] | |
nth [Biocaml_seq] | nth t i returns the i th nucleic acid in sequence t .
|
num_bins [Biocaml_histogram] |
Number of bins.
|
num_probes [Biocaml_bpmap] |
Number of PM/MM probe pairs in given BPMAP.
|
O | |
odd [Biocaml_math] |
True if given integer is odd.
|
of_ascii [Biocaml_solexa_score] | of_ascii x returns the PHRED score encoded by ASCII character
x .
|
of_ascii [Biocaml_phred_score] | of_ascii ~offset x returns the PHRED score encoded by ASCII
character x .
|
of_ascii_exn [Biocaml_phred_score] |
Like
of_ascii but may raise
Error _ if x does not represent a valid score.
|
of_buffer [Biocaml_seq] |
Make sequence from buffer.
|
of_buffer_unsafe [Biocaml_seq] | |
of_channel [Biocaml_sgr] | |
of_channel [Biocaml_lines] |
Get a stream of lines out of an input-channel.
|
of_char_stream [Biocaml_lines] |
Parse a stream of characters into a stream of lines.writing the
|
of_chr_lists [Biocaml_sgr] | |
of_file [Biocaml_sgr] | |
of_file [Biocaml_mzData] | of_file fname returns the spectra contained in the file
fname .
|
of_file [Biocaml_cel] |
Parse given file if possible.
|
of_file [Biocaml_bpmap] | of_file file parses file .
|
of_file [Biocaml_bar] |
Parse file.
|
of_file_opt [Biocaml_cel] |
Parse given file if possible.
|
of_function [Biocaml_transform] | of_function f is like identity () but the transform outputs
are passed to the function f .
|
of_int [Biocaml_sam.Flags] | |
of_int [Biocaml_romanNum] |
Convert integer to roman numeral if possible.
|
of_int_exn [Biocaml_romanNum] |
Like
of_int but raise Bad if unable to convert integer.
|
of_int_exn [Biocaml_phred_score] | of_int_exn x returns the PHRED score with the same value x , but
assures that x is non-negative.
|
of_line [Biocaml_table.Row] |
Parse a
Line.t into a row while specifying a format .
|
of_list [Biocaml_iset] |
Build a ISet.t out of a list or enum of ranges
|
of_list [Biocaml_sgr] | |
of_object [Biocaml_transform] | |
of_probability [Biocaml_solexa_score] | of_probability ~f x returns -10 * log_10(x/(1-x)) , which is the
definition of Solexa scores.
|
of_probability [Biocaml_phred_score] | of_probability ~f x returns -10 * log_10(x) , which is the
definition of PHRED scores.
|
of_probability_exn [Biocaml_phred_score] |
See
of_probability
|
of_range_list [Biocaml_rSet] |
Construct the set of integers representing the union of integers in all given ranges.
|
of_solexa_score [Biocaml_phred_score] | of_solexa_score x converts Solexa score x to a PHRED
score.
|
of_stream [Biocaml_iset] | |
of_stream [Biocaml_genomeMap.LMap] | |
of_stream [Biocaml_genomeMap.LSet] | |
of_stream [Biocaml_genomeMap.Selection] | of_stream e computes a selection as the union of the locations contained in e
|
of_stream [Biocaml_accu.Relation] | |
of_stream [Biocaml_accu.Counter] | |
of_string [Biocaml_wig.Tags] |
Parse tags (for now S-Expressions).
|
of_string [Biocaml_tags] |
Parse a tag specification (the format is, for now, based on
S-Expressions, but this will change).
|
of_string [Biocaml_table.Row.Tags] |
Parse the description of the tags (for now S-Expressions).
|
of_string [Biocaml_strandName] |
Convert string to chromosome name if possible.
|
of_string [Biocaml_seq] |
Make sequence from string.
|
of_string [Biocaml_romanNum] |
Parse string as a roman numeral if possible.
|
of_string [Biocaml_gff.Tags] |
Parse tags (for now S-Expressions).
|
of_string [Biocaml_fasta.Tags] |
Parse tags (for now S-Expressions).
|
of_string_exn [Biocaml_strandName] |
Like
of_string but raise Bad if conversion not possible.
|
of_string_exn [Biocaml_romanNum] |
Like
of_string but raise Bad if unable to parse string.
|
of_string_unsafe [Biocaml_seq] |
Make a sequence from given buffer or string.
|
of_string_unsafe [Biocaml_line] |
Return the given string without checking that it is a line.
|
on_error [Biocaml_transform] |
Like
on_output but on the erroneous part of the output.
|
on_input [Biocaml_transform] | on_input f t returns a transform that converts its inputs with
f and feeds the results to t .
|
on_ok [Biocaml_transform] |
Like
on_output but on the successful part of the output.
|
on_output [Biocaml_transform] | on_output t f returns a transform that behaves like t except
the outputs are first converted by f .
|
open_out_safe [Biocaml_internal_pervasives] |
Like
open_out but will not overwrite existing file.
|
optional_content_of_sexp [Biocaml_sam] | |
optional_content_parsing_of_sexp [Biocaml_sam.Error] | |
optional_content_value_of_sexp [Biocaml_sam] | |
output_error [Biocaml_internal_pervasives.Result] | |
output_ok [Biocaml_internal_pervasives.Result] | |
output_result [Biocaml_internal_pervasives.Result] | |
overlap [Biocaml_range] | overlap u v returns amount of overlap between two ranges.
|
P | |
parse_cigar [Biocaml_bam] |
Parse CIGAR operations from a string (c.f.
|
parse_cigar_of_sexp [Biocaml_bam.Error] | |
parse_cigar_text [Biocaml_sam] |
Parse CIGAR operations from a string.
|
parse_error_to_string [Biocaml_vcf] | |
parse_header_line [Biocaml_sam] |
Parse a header line form a string.
|
parse_of_sexp [Biocaml_sam.Error] | |
parse_optional [Biocaml_bam] |
Parse optional content from a string (c.f.
|
parse_optional_content [Biocaml_sam] |
Parse optional content from a “tokenized” string.
|
parse_optional_of_sexp [Biocaml_bam.Error] | |
parsing_base_of_sexp [Biocaml_bed.Error] | |
parsing_error_to_string [Biocaml_wig.Error] |
Convert a
parsing error to a string.
|
parsing_of_sexp [Biocaml_wig.Error] | |
parsing_of_sexp [Biocaml_track.Error] | |
parsing_of_sexp [Biocaml_gff.Error] | |
parsing_of_sexp [Biocaml_bed.Error] | |
parsing_spec_of_sexp [Biocaml_bed] | |
partition [Biocaml_iset] |
partitions the input set into two sets with elements that satisfy
the predicate and those that don't
|
pcr_or_optical_duplicate [Biocaml_sam.Flags] | |
pearson [Biocaml_math] | pearson arr1 arr2 computes the Pearson product-moment correlation coefficient of two float arrays.
|
peek_line [Biocaml_lines.Buffer] |
Peek at the next line, without removing it from the buffer.
|
pm [Biocaml_cel] |
Similar to
Biocaml_cel.data but the data returned are the PM mean intensity
values in cels .
|
pm_mm [Biocaml_cel] |
Similar to
Biocaml_cel.data but the data returned are the PM-MM mean
intensity values in cels .
|
positive_predictive_value [Biocaml_roc] | |
prediction_values [Biocaml_math] | prediction_values tp tn fp fn takes 4 arguments: the number of true-positives tp , true-negatives tn , false-positives fp , and false-negatives fn .
|
print [Biocaml_interval_tree] |
Used for debugging purpose, should be removed in the long run
|
print_bug [Biocaml_msg] |
Print an error, warning, or bug.
|
print_err [Biocaml_msg] | |
print_warn [Biocaml_msg] | |
product [Biocaml_accu] | product filter f l1 l2 computes an histogram of values returned by f
when it is applied for all combinations of elements in l1 and
l2 such that the predicate filter is true
|
pseudomedian [Biocaml_math] |
Pseudomedian is the median of all pairwise averages of values in given array (not including self-pairs).
|
pwfold [Biocaml_genomeMap.LMap_spec] |
a constant interval of an LMap
lm is a range intersecting lm and
that do not contain any start or end of a range from lm .
|
Q | |
quantile_normalization [Biocaml_math] |
Input matrix
m should be arranged such that m.(i).(j) is the i th measurement in experiment j .
|
queued_lines [Biocaml_lines.Buffer] |
Get the number of lines ready-to-use in the buffer/queue.
|
R | |
range [Biocaml_internal_pervasives.Array] | range xs is the stream of all valid indices in xs
|
range [Biocaml_math] | range step first last returns array [|first; first +.
|
range_floats [Biocaml_math] | |
range_ints [Biocaml_math] | |
ranges [Biocaml_iset] |
Returns a list of all contiguous ranges in the set
|
rank [Biocaml_math] | rank arr returns an array of ranked values, where ties are given the mean of what the rank would otherwise be.
|
raw_alignment_of_sexp [Biocaml_bam] | |
raw_bam_of_sexp [Biocaml_bam.Error] | |
raw_item_of_sexp [Biocaml_fasta] | |
raw_item_of_sexp [Biocaml_bam] | |
raw_to_item [Biocaml_sam.Transform] |
Create a transform that lifts
raw_item s to item s
|
raw_to_item [Biocaml_bam.Transform] |
Create a transform that lifts
raw_item s to the higher-level representation
defined in the Biocaml_sam module.
|
raw_to_item_of_sexp [Biocaml_sam.Error] | |
raw_to_item_of_sexp [Biocaml_bam.Error] | |
raw_to_string [Biocaml_sam.Transform] |
Create a printing "stoppable" transform.
|
raw_to_string [Biocaml_bam.Transform] |
Create a transform that “prints”
raw_item s in the BAM format.
|
record_of_sexp [Biocaml_gff] | |
reference_sequence [Biocaml_sam] |
Create a reference sequence.
|
relation [Biocaml_accu] | |
remove [Biocaml_iset] |
Remove an element from the given set, returning a new set
|
remove_range [Biocaml_iset] | remove_range lo hi t removes a range of elements from the given set, returning a new set
|
reset [Biocaml_histogram] |
Return histogram with same bins but all counts reset to 0.0.
|
rev_fwd [Biocaml_strandName] |
Return "rev" or "fwd".
|
reverse [Biocaml_internal_pervasives.Order] | |
reverse_complement [Biocaml_pwm] |
Reverse complement of a PWM
|
reversep [Biocaml_internal_pervasives.Order] | |
rms [Biocaml_math] |
Root mean square.
|
row [Biocaml_math] | row m i returns the i th row of matrix m .
|
row_to_string [Biocaml_bpmap] |
String representation of row in same format as required by specification.
|
rstrip [Biocaml_line] | |
S | |
scale [Biocaml_bar] |
Return scale data is reported in, e.g.
|
scan [Biocaml_pwm] | scan mat seq tol returns the list of positions (with
corresponding scores) such that the alignment score
of mat is superior to tol
|
search [Biocaml_entrez.Make.Gene] | |
search [Biocaml_entrez.Make.Pubmed] | |
search [Biocaml_entrez.Make.PubmedSummary] | |
secondary_alignment [Biocaml_sam.Flags] | |
section [Biocaml_bar] | section t name returns the section named name .
|
sectioni [Biocaml_bar] | sectioni t i returns the i 'th section.
|
sections [Biocaml_bar] |
Return all sections in
t .
|
segment_unmapped [Biocaml_sam.Flags] | |
sensitivity [Biocaml_roc] | |
separators [Biocaml_table.Row.Tags] |
Get the list of separators defined in
t .
|
seq_is_reverse_complemented [Biocaml_sam.Flags] | |
set_col [Biocaml_pos] |
Set the file name, line number, or column number.
|
set_file [Biocaml_pos] | |
set_line [Biocaml_pos] | |
sexp_of_alignment [Biocaml_sam] | |
sexp_of_bed_graph_value [Biocaml_wig] | |
sexp_of_char_seq [Biocaml_fasta] | |
sexp_of_cigar_op [Biocaml_sam] | |
sexp_of_comment [Biocaml_wig] | |
sexp_of_file_format [Biocaml_tags] | |
sexp_of_fixed_step [Biocaml_wig] | |
sexp_of_input_error [Biocaml_tags.Input_transform] | |
sexp_of_int_seq [Biocaml_fasta] | |
sexp_of_item [Biocaml_wig] | |
sexp_of_item [Biocaml_table.Row] | |
sexp_of_item [Biocaml_sam] | |
sexp_of_item [Biocaml_psl] | |
sexp_of_item [Biocaml_lines] | |
sexp_of_item [Biocaml_gff] | |
sexp_of_item [Biocaml_fastq] | |
sexp_of_item [Biocaml_fasta] | |
sexp_of_item [Biocaml_bed] | |
sexp_of_item_to_raw [Biocaml_sam.Error] | |
sexp_of_item_to_raw [Biocaml_bam.Error] | |
sexp_of_item_type [Biocaml_table.Row] | |
sexp_of_line_parsing [Biocaml_table.Row.Error] | |
sexp_of_optional_content [Biocaml_sam] | |
sexp_of_optional_content_parsing [Biocaml_sam.Error] | |
sexp_of_optional_content_value [Biocaml_sam] | |
sexp_of_output_error [Biocaml_tags.Output_transform] | |
sexp_of_parse [Biocaml_sam.Error] | |
sexp_of_parse_cigar [Biocaml_bam.Error] | |
sexp_of_parse_optional [Biocaml_bam.Error] | |
sexp_of_parsing [Biocaml_wig.Error] | |
sexp_of_parsing [Biocaml_track.Error] | |
sexp_of_parsing [Biocaml_gff.Error] | |
sexp_of_parsing [Biocaml_bed.Error] | |
sexp_of_parsing_base [Biocaml_bed.Error] | |
sexp_of_parsing_spec [Biocaml_bed] | |
sexp_of_raw_alignment [Biocaml_bam] | |
sexp_of_raw_bam [Biocaml_bam.Error] | |
sexp_of_raw_item [Biocaml_fasta] | |
sexp_of_raw_item [Biocaml_bam] | |
sexp_of_raw_to_item [Biocaml_sam.Error] | |
sexp_of_raw_to_item [Biocaml_bam.Error] | |
sexp_of_record [Biocaml_gff] | |
sexp_of_string_to_raw [Biocaml_sam.Error] | |
sexp_of_string_to_raw_item [Biocaml_fasta.Error] | |
sexp_of_t [Biocaml_zip.Error] | |
sexp_of_t [Biocaml_wig.Tags] | |
sexp_of_t [Biocaml_wig.Error] | |
sexp_of_t [Biocaml_track.Error] | |
sexp_of_t [Biocaml_table.Row.Error] | |
sexp_of_t [Biocaml_table.Row.Tags] | |
sexp_of_t [Biocaml_table.Row] | |
sexp_of_t [Biocaml_sam.Error] | |
sexp_of_t [Biocaml_lines.Error] | |
sexp_of_t [Biocaml_line] | |
sexp_of_t [Biocaml_gff.Tags] | |
sexp_of_t [Biocaml_gff.Error] | |
sexp_of_t [Biocaml_fastq.Error] | |
sexp_of_t [Biocaml_fasta.Error] | |
sexp_of_t [Biocaml_fasta.Tags] | |
sexp_of_t [Biocaml_bed.Error] | |
sexp_of_t [Biocaml_bam.Error] | |
sexp_of_t_type [Biocaml_table.Row] | |
sexp_of_to_bed_graph [Biocaml_wig.Error] | |
sexp_of_unzip [Biocaml_zip.Error] | |
sexp_of_variable_step [Biocaml_wig] | |
shuffle [Biocaml_math] | shuffle arr takes an array and randomly shuffles it.
|
singleton [Biocaml_iset] |
Return the singleton set containing only the given element
|
size [Biocaml_rSet] |
Number of elements in set.
|
size [Biocaml_range] | size v returns the number of integers in v , i.e.
|
size [Biocaml_genomeMap.Selection] | |
slice [Biocaml_seq] | slice first last t returns the sub-sequence, or slice, of t
starting from index first to last (inclusive).
|
spearman [Biocaml_math] | spearman arr1 arr2 computes the Spearman rank correlation coefficient of two float arrays.
|
specification_of_string [Biocaml_fasta.Random] |
Parse a
specification from a string .
|
specificity [Biocaml_roc] | |
split [Biocaml_line] | |
split_and_merge [Biocaml_transform] | split_and_merge t u ~split ~merge returns a transform whose
input is split using split , passing the result either to t or u ,
and then the outputs of t and u are combined using merge .
|
stdv [Biocaml_math] |
Standard deviation.
|
stop [Biocaml_transform] | stop t declares t to be stopped, which means subsequent calls to:
|
stream [Biocaml_accu.Relation] | |
stream [Biocaml_accu.Counter] | |
stream [Biocaml_accu] | |
strict_after [Biocaml_range] | strict_after u v is equivalent to strict_before v u .
|
strict_before [Biocaml_range] | strict_before u v is true if u.lo < v.lo && u.hi < v.hi .
|
strict_cell_type [Biocaml_table.Row.Tags] |
Tell whether one should be strict about the types of the cells
(defined with
`format _ ).
|
strict_row_length [Biocaml_table.Row.Tags] |
Tell whether one should be strict about the minimal number of
cells per row (defined with
`format _ ).
|
strict_subset [Biocaml_range] | strict_subset u v is true if u is a strict subset of v .
|
strict_superset [Biocaml_range] | strict_superset u v is true if u is a strict superset of v .
|
string_content_to_string [Biocaml_track.Transform] |
Create a printer for track files containing
`content line lines.
|
string_to_bed [Biocaml_track.Transform] |
Create a composite parser for UCSC Bed(Graph) files.
|
string_to_char_seq_raw_item [Biocaml_fasta.Transform] |
Parse a stream of strings as a char_seq FASTA file.
|
string_to_gff [Biocaml_track.Transform] |
Create a composite parser for UCSC GFF files.
|
string_to_int_seq_raw_item [Biocaml_fasta.Transform] |
Parse a stream of strings as an int_seq FASTA file.
|
string_to_item [Biocaml_wig.Transform] |
Create the parsing
Biocaml_transform.t .
|
string_to_item [Biocaml_vcf.Transform] | |
string_to_item [Biocaml_psl.Transform] | |
string_to_item [Biocaml_lines.Transform] |
Return a transform that converts a stream of arbitrary strings
to a stream of lines.
|
string_to_item [Biocaml_gff.Transform] |
Create a parsing
Biocaml_transform.t for a given version.
|
string_to_item [Biocaml_fastq.Transform] |
Create a
Biocaml_transform.t from arbitrary strings to
item values.
|
string_to_item [Biocaml_bed.Transform] |
Create a
Biocaml_transform.t -based parser, while providing the
format of the additional columns (default `strings ).
|
string_to_lines [Biocaml_line] | string_to_lines s splits s on newline characters, returning
the resuling list of lines.
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string_to_raw [Biocaml_sam.Transform] |
Create a parsing "stoppable" transform.
|
string_to_raw [Biocaml_bam.Transform] |
Create a transform that parses a BAM file.
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string_to_raw_item_of_sexp [Biocaml_fasta.Error] | |
string_to_raw_of_sexp [Biocaml_sam.Error] | |
string_to_string_content [Biocaml_track.Transform] |
Create a parser that gets the "track", comment, and "browser"
lines and puts the other lines in
`content _ .
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string_to_wig [Biocaml_track.Transform] |
Create a composite parser for UCSC WIG files.
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strip [Biocaml_line] | |
subset [Biocaml_iset] | subset t u returns true if t is a subset of u
|
subset [Biocaml_rSet] | subset s t returns true if s is a subset of t .
|
subset [Biocaml_range] | subset u v is true if u is a subset of v .
|
superset [Biocaml_range] | superset u v is true if u is a superset of v .
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T | |
t_of_sexp [Biocaml_zip.Error] | |
t_of_sexp [Biocaml_wig.Tags] | |
t_of_sexp [Biocaml_wig.Error] | |
t_of_sexp [Biocaml_track.Error] | |
t_of_sexp [Biocaml_table.Row.Error] | |
t_of_sexp [Biocaml_table.Row.Tags] | |
t_of_sexp [Biocaml_table.Row] | |
t_of_sexp [Biocaml_sam.Error] | |
t_of_sexp [Biocaml_lines.Error] | |
t_of_sexp [Biocaml_line] | |
t_of_sexp [Biocaml_gff.Tags] | |
t_of_sexp [Biocaml_gff.Error] | |
t_of_sexp [Biocaml_fastq.Error] | |
t_of_sexp [Biocaml_fasta.Error] | |
t_of_sexp [Biocaml_fasta.Tags] | |
t_of_sexp [Biocaml_bed.Error] | |
t_of_sexp [Biocaml_bam.Error] | |
t_to_string [Biocaml_fastq.Error] |
Transform error to a human-readable string.
|
t_type_of_sexp [Biocaml_table.Row] | |
tandem [Biocaml_pwm] | tandem orientation spacer cm1 cm2 bg builds a PWM by constructing
a composite motif: it builds mat1 the PWM from cm1 under background bg
(resp.
|
tick [Biocaml_accu.Counter] | |
to_arabic [Biocaml_chr] | to_arabic s returns the canonical Arabic representation of s .
|
to_ascii [Biocaml_solexa_score] | to_ascii t encodes t as an ASCII character.
|
to_ascii [Biocaml_phred_score] | to_ascii t encodes t as an ASCII character.
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to_ascii_exn [Biocaml_phred_score] | to_ascii_exn t encodes t as an ASCII character.
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to_backwards_stream [Biocaml_interval_tree] | |
to_bed_graph_of_sexp [Biocaml_wig.Error] | |
to_channel [Biocaml_sgr] | |
to_channel [Biocaml_lines] |
Write a stream of lines to an output-channel.
|
to_chr_lists [Biocaml_sgr] |
Outer list will be in ascending order by
chr , and inner lists will be in ascending order by coord .
|
to_file [Biocaml_sgr] |
Items will be printed in ascending order by
(chr,coord) .
|
to_file [Biocaml_bpmap] | to_file file t prints t to file in format required by specification.
|
to_int [Biocaml_romanNum] |
Convert roman numeral to integer.
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to_int [Biocaml_phred_score] |
Convert a phred score to an integer.
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to_line [Biocaml_table.Row] |
Write the row to a
Line.t .
|
to_list [Biocaml_sgr] |
Items will be returned in ascending order by
(chr,coord) .
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to_list [Biocaml_rSet] |
Return set of integers as a list.
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to_list [Biocaml_range] | to_list v returns the set of integers contained in v , in ascending order.
|
to_list [Biocaml_histogram] |
Return a list of all bin/count pairs.
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to_list [Biocaml_bpmap] | |
to_list [Biocaml_bar] |
Return the data as a list of triplets (chr,pos,v) representing the
chromosome name, probe position, and value.
|
to_object [Biocaml_transform] | |
to_pair [Biocaml_range] | to_pair t returns the int * int pair.
|
to_probability [Biocaml_solexa_score] | to_probablity x converts x to a probablity score.
|
to_probability [Biocaml_phred_score] | to_probablity x converts x to a probablity score.
|
to_range_list [Biocaml_rSet] |
Return set of integers as a minimal list of non-overlapping ranges in ascending order by their coordinates.
|
to_roman [Biocaml_chr] | to_roman s returns the canonical Roman representation of s .
|
to_roman_exn [Biocaml_chr] | |
to_solexa_score [Biocaml_phred_score] | to_solexa_score t converts PHRED score t to a Solexa
score.
|
to_stream [Biocaml_iset] |
Enumerates all contiguous ranges in the set
|
to_stream [Biocaml_interval_tree] | |
to_stream [Biocaml_genomeMap.LMap_spec] | |
to_stream [Biocaml_genomeMap.Signal] |
enumeration over all constant intervals of the function, in increasing order
|
to_stream [Biocaml_genomeMap.LMap] | |
to_stream [Biocaml_genomeMap.LSet] | |
to_stream [Biocaml_genomeMap.Selection] | |
to_stream_fun [Biocaml_transform] | to_stream_fun t returns a function f that behaves like
t but the inputs and outputs are on standard OCaml streams.
|
to_string [Biocaml_wig.Tags] |
Serialize tags (for now S-Expressions).
|
to_string [Biocaml_tags] |
Convert a
t ag to its string specification.
|
to_string [Biocaml_table.Row.Tags] |
Serialize tags.
|
to_string [Biocaml_strandName] |
String representation of a strand.
|
to_string [Biocaml_seq] |
Return string representation of sequence.
|
to_string [Biocaml_romanNum] |
String representation of a roman numeral.
|
to_string [Biocaml_range] |
String representation of an range, intended only for human legibility.
|
to_string [Biocaml_pos] |
String representation of a position.
|
to_string [Biocaml_msg.Tree] | |
to_string [Biocaml_gff.Tags] |
Serialize tags (for now S-Expressions).
|
to_string [Biocaml_fasta.Tags] |
Serialize tags (for now S-Expressions).
|
to_string [Biocaml_entrez.Make.Object_id] | |
to_tag [Biocaml_tags] |
Do a practical coercion.
|
totalify [Biocaml_internal_pervasives.Order] | |
transpose [Biocaml_math] | transpose m transpose the given matrix m .
|
trim [Biocaml_fastq.Transform] |
Create a
Biocaml_transform.t that trims FASTQ items.
|
try_finally_exn [Biocaml_internal_pervasives] | try_finally_exn fend f a will run x = f a , then run fend
a , and finally return x .
|
U | |
unescape [Biocaml_internal_pervasives.Url] |
Convert a string containing
"%HX" escaped characters to a normal
string.
|
union [Biocaml_iset] |
Compute the union of two sets.
|
union [Biocaml_rSet] |
Set union.
|
union [Biocaml_range] | union u v returns the ranges representing the union of u and v .
|
union [Biocaml_genomeMap.LMap_spec] | |
union [Biocaml_genomeMap.Selection] | |
unit_to_random_char_seq_raw_item [Biocaml_fasta.Random] |
Create a transformation that generates random
char_seq
raw_item values according to the specification.
|
unknown [Biocaml_pos] |
Represents an unknown position.
|
until [Biocaml_iset] | until ~n t returns the portion of t in the range min_int, n
|
unzip [Biocaml_zip.Transform] |
Create a transform that uncompresses a stream.
|
unzip_in_channel [Biocaml_zip] |
Decompress an Input Channel.
|
unzip_in_channel_exn [Biocaml_zip] |
Like
unzip_in_channel but calls to Stream.next may raise
Error e exceptions.
|
unzip_of_sexp [Biocaml_zip.Error] | |
V | |
variable_step_of_sexp [Biocaml_wig] | |
variance [Biocaml_math] |
Variance.
|
version [Biocaml_about] | |
W | |
warn [Biocaml_msg] | |
while_ok [Biocaml_internal_pervasives.Result] |
Map the function
f on the list until the first error is
met.
|
wig_to_string [Biocaml_track.Transform] |
Create a printer for track files containing WIG lines.
|
wilcoxon_rank_sum [Biocaml_math] | wilcoxon_rank_sum ~alpha=(float) arr1 arr2 performs the Wilcoxon rank sum test on two arrays with an optional argument alpha, set to 0.05 by default.
|
wilcoxon_rank_sum_to_p [Biocaml_math] |
Performs the wilcoxon rank sum on two float arrays and returns the p-value.
|
wilcoxon_rank_sum_to_z [Biocaml_math] |
As below, except returns a z value.
|
Z | |
zip [Biocaml_zip.Transform] |
Create a transform that writes compressed data.
|
zip_in_channel [Biocaml_zip] |
Compress an Input Channel.
|
zlib_buffer_size [Biocaml_zip.Default] |
The default size of the internal buffer used by the ZLib library.
|