Index of values

add lo hi v t adds the interval (lo, hi) labeled with value v to the contents of t.

add accu x y updates the value in accu for the bin of x by an increment y

add_attribute x y r adds attribute x with value y in r.

add_child t x inserts x as the right-most child of t.

after u v is equivalent to before v u.

Name of algorithm used to generate scores.

Version number of algorithm used.

Return true if all pairs of given ranges are positionally comparable.

Return true if any pair of given ranges overlap each other.

arabic s returns the canonical Arabic representation of s.

List of attributes defined for the given row.

auc e computes the area above the X-axis and under the piecewise linear curve passing through the points in e.

background_of_sequence seq pc estimates the base frequency in seq using pc as pseudo-counts.

before u v is true if strict_before u v || equal u v.

bin hist i returns the ith bin of hist.

Create a string communicating an error, warning, or bug.

Used for debugging purpose, should be removed in the long run

closest loc lmap returns the location in lmap which is the closest to loc, along with its annotation and the actual (minimal) distance.

Cumulative distribution function.

Return the file name, line number, or column number.

Names of columns in BPMAP file, in the order required by specification.

column m i extracts the ith column of matrix m.

Return the start character for the given comments.

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 by ranges' hi bounds, ignoring lo bounds.

Compare by ranges' lo bounds, ignoring hi bounds.

Return order between lo bounds unless they are equal, in which case return order between hi bounds.

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.

concat t1 t2 returns a type representing the lines t1 followed by t2.

concat a b concatenates comment lines a and b such that a is followed by b.

Probe coordinate convention used.

Copy histogram.

count hist i returns the count the ith bin.

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.

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).

Return the type of data, either "signal" or "p-value".

This function generates random lists and uses them as arguments for test.

delete_attribute x r deletes all occurrences of attribute x in r.

Set difference.

the empty tree

Empty track line.

The empty set.

empty c is the empty list of comment lines, but with the specification that c will be used as the start character.

enumeration over all constant intervals of the function, in increasing order

Return start character and enumeration of comment lines in given t.

Returns enumeration of fastq records in given input.

Returns comments and enumeration of fasta records in given input.

Returns comments and enumeration of fasta records in given path.

epsilon f init fin applies f n fin to all numbers from init to fin and adds them up.

Returned enum behaves identically to given one except that its use will raise PosError when accessing its element raises an exception e.

function evaluation at some point in the genome

True if given integer is even.

exp_assoc_list dat returns a list associating each integer i with the list of values associated with all ranges overlapping i in dat.

Self-explanatory.

Identical to scan but directly implemented in C

filter_comments_prefix c e removes the first lines of e that are comments and builds a Comment.t with it, which is returned along with the rest of the enum e

find x t returns the value of tag x in t.

find t a returns the value of attribute a, or raises Not_found if no such attribute.

find_bin_index hist x returns the index of the bin in hist containing x.

find_closest lo hi t returns the interval in t which is at minimal distance of the interval [lo;hi].

find_min_range v pred i finds the minimum sized range within v centered around i that satisfies pred.

find_min_window a pred i finds the minimum sized window within a centered around index i that satisfies pred.

TO DO: fill in this documentation.

find_regions ~max_gap pred a returns an array of (first,last) index pairs denoting boundaries (inclusive) of regions found in a.

Uniform distribution over A, C, G, T

Methods for creating a position.

fold guaranteed on increasing order keywise, and for each key

fold guaranteed on increasing order keywise, and for each key

folds on constant intervals of the function, in increasing order

fold_file f init file accumulates the result of applying f to each row of file.

see String.fold_left.

String.fold_lefti

hide, dense, pack, squish, and full each take a string that should either be "all" or a space separated list of track names.

gap u v returns the size of the gap between u and v.

File path of bpmap file used to generate scores.

get accu x returns the value associated to b in accu.

get_attribute r x returns the value of attribute x.

get_attributel r x returns the values of the attribute named x in row r.

has_attribute r x returns true if attribute x is defined in r.

Return histogram of values using cmp (default = Pervasives.compare) for comparison.

idxsort cmp a is like Array.sort but a is unaltered, and instead an array of the indices in sorted order is returned.

ifold f a t folds over data rows in intensity section of t.

iiter f t iterates over the rows in intensity section of t.

in_range hist x is true if x greater than or equal to minimum hist and strictly less than maximum hist.

Returns an sb_model read from input stream

increment delt hist x increments the count of the bin containing x by delt (default is 1.0).

incrl pos k increments the line number of pos by k.

index_by_attribute x returns a mapping from the values of attribute x to those rows with that value.

Set intersection.

intersect u v returns the range representing the intersection of u and v.

intersects a b t returns true if one interval in t intersects with the interval [a;b].

intersects loc lmap returns true if loc has a non-empty intersection with one of the locations in lmap, and returns false otherwise

intersects loc sel returns true if loc has a non-empty intersection with sel, and false otherwise.

Like of_string but simply returns true if given string can be parsed as valid comment lines.

Return true if given set is empty.

True if given character represents one of the allowed nucleic acid codes, case-insensitive.

Length of sequence.

Logarithm.

Base 10 logarithm.

Base 2 logarithm.

Lower tail quantile for standard normal distribution function.

Median absolute deviation (MAD).

Major version number.

Given an enum pos (resp.

make l u returns the range from l to u.

Builds a PWM from a count_matrix and a background

make cmp bins returns a new histogram from the given bins, all initialized to a count of 0.0.

Like make but returns None instead of raising exception.

make_uniform min max n returns a histogram with n bins uniformly dividing up the range from min to max.

mass p return the mass of the precursor p without charge.

Returns a string with sb_math converted into a S-expression

Return maximum value in given array.

String explaining OCaml's array length limitation on 32-bit machines.

Return maximum gap between adjacent pairs of given ranges.

Upper limit of the maximum bin.

Mean.

Median.

mem x t returns true if t contains a value for tag x.

mem t a x returns true if a is assigned value x in t.

member t k returns true if t contains k.

Return minimum value in given array.

Lower limit of the minimum bin.

Minor version number.

Return "-" or "+".

Similar to Biocaml_cel.data but the data returned are the MM mean intensity values in cels.

nth t i returns the ith nucleic acid in sequence t.

Number of bins.

Number of PM/MM probe pairs in given BPMAP.

True if given integer is odd.

of_ascii x returns the PHRED score encoded by ASCII character x.

of_ascii ~offset x returns the PHRED score encoded by ASCII character x.

Make sequence from buffer.

of_enum e computes a selection as the union of the locations contained in e

of_file fname returns the spectra contained in the file fname.

of_file file parses file.

Parse given file if possible.

of_file file parses file.

Parse file.

Parse given file if possible.

Default itags is:

Convert integer to roman numeral if possible.

of_int x returns the PHRED score with the same value x, but assures that x is non-negative.

Like of_int but raise Bad if unable to convert integer.

Construct WIG data from given pt's.

of_list l sets a to x for every (a,x) pair in l.

of_probability ~f x returns -10 * log_10(x/(1-x)), which is the definition of Solexa scores.

of_probability ~f x returns -10 * log_10(x), which is the definition of PHRED scores.

Construct the set of integers representing the union of integers in all given ranges.

of_solexa_score x converts Solexa score x to a PHRED score.

Parse given string as list of tags.

Creates a list of lines by splitting given string on newline characters.

Parse string to track line.

Convert string to chromosome name if possible.

Make sequence from string.

Parse string as a roman numeral if possible.

of_string c s creates list of lines by splitting given string on newline characters.

Like of_string but raise Bad if conversion not possible.

Like of_string but raise Bad if unable to parse string.

Default itags are:

Make a sequence from given buffer or string.

overlap u v returns amount of overlap between two ranges.

pearson arr1 arr2 computes the Pearson product-moment correlation coefficient of two float arrays.

Similar to Biocaml_cel.data but the data returned are the PM mean intensity values in cels.

Similar to Biocaml_cel.data but the data returned are the PM-MM mean intensity values in cels.

position chr start end returns the browser line "chr:start-end".

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.

Used for debugging purpose, should be removed in the long run

Print an error, warning, or bug.

Pseudomedian is the median of all pairwise averages of values in given array (not including self-pairs).

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.

Input matrix m should be arranged such that m.(i).(j) is the ith measurement in experiment j.

range step first last returns array [|first; first +.

rank arr returns an array of ranked values, where ties are given the mean of what the rank would otherwise be.

(year,month,day) of the current release.

Return histogram with same bins but all counts reset to 0.0.

Return "rev" or "fwd".

Reverse complement of a PWM

Root mean square.

roman s returns the canonical Roman representation of s.

row m i returns the ith row of matrix m.

String representation of row in same format as required by specification.

Return scale data is reported in, e.g.

scan mat seq tol returns the list of positions (with corresponding scores) such that the alignment score of mat is superior to tol

section t name returns the section named name.

sectioni t i returns the i'th section.

Return all sections in t.

set t a x sets attribute a to value x in t.

set_attribute x y r sets attribute x to y in r, deleting any previous values.

Set the file name, line number, or column number.

shuffle arr takes an array and randomly shuffles it.

Number of elements in set.

size v returns the number of integers in v, i.e.

slice first last t returns the sub-sequence, or slice, of t starting from index first to last (inclusive).

spearman arr1 arr2 computes the Spearman rank correlation coefficient of two float arrays.

Standard deviation.

strict_after u v is equivalent to strict_before v u.

strict_before u v is true if u.lo < v.lo && u.hi < v.hi.

strict_subset u v is true if u is a strict subset of v.

strict_superset u v is true if u is a strict superset of v.

subset s t returns true if s is a subset of t.

subset u v is true if u is a subset of v.

superset u v is true if u is a superset of v.

tag_is x y t returns true if x=y in t, or false if tag x assigned some other value or not found in t.

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.

test ul vl compares performance and correctness of set intersection and union.

to_ascii t encodes t as an ASCII character.

to_ascii t encodes t as an ASCII character.

Like to_file but print to channel.

Outer list will be in ascending order by chr, and inner lists will be in ascending order by coord.

to_file ~fmt t file prints t to file.

Items will be printed in ascending order by (chr,coord).

to_file file t prints t to file in format required by specification.

Convert roman numeral to integer.

Extract data as a flat list.

Return list of attribute=value pairs.

Items will be returned in ascending order by (chr,coord).

Return set of integers as a list.

to_list v returns the set of integers contained in v, in ascending order.

Return a list of all bin/count pairs.

Return the data as a list of triplets (chr,pos,v) representing the chromosome name, probe position, and value.

Partitions annotations by chromosome.

to_pair t returns the int * int pair.

to_probablity x converts x to a probablity score.

to_probablity x converts x to a probablity score.

Return set of integers as a minimal list of non-overlapping ranges in ascending order by their coordinates.

to_solexa_score t converts PHRED score t to a Solexa score.

to_sqlite t writes contents of t into a SQLite database, and returns the handle to it.

String representation of a position.

Return string representation of browser lines.

Return string representing track line in required format.

String representation of a strand.

Return string representation of sequence.

String representation of a roman numeral.

String representation of an range, intended only for human legibility.

Return string representation of comment lines.

Transpose given matrix m.

Set union.

union u v returns the ranges representing the union of u and v.

Represents an unknown position.

unset t a deletes attribute a from t.

Returns true if t is a valid wiggle track line.

Variance.

String representation of version.

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.

Performs the wilcoxon rank sum on two float arrays and returns the p-value.

As below, except returns a z value.