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Module Biocaml_bar (.ml)

Affymetrix's BAR files. Their Tiling Analysis Software (TAS) produces BAR files in binary format but this module supports only the text format generated by selecting the "Export probe analysis as TXT" option.

module Biocaml_bar:
sig
type t
Type of a BAR file, which can be thought of as a header plus set of sections.
exception Bad of string
type section = private {
   sec_num : int; (*order in which section appears in file, first section is numbered 1*)
   sec_name : string; (*chromosome name relative to which coordinates are given*)
   sec_data : (int * float) list; (*pairs of coordinate-score data*)
} 
val of_file : string -> t
Parse file. Raise Bad if there are parse errors.
val to_list : t -> (string * int * float) list
Return the data as a list of triplets (chr,pos,v) representing the chromosome name, probe position, and value. Will be returned in ascending order by (chr,pos).
val section : t -> string -> section
section t name returns the section named name. Raise Failure if no such section.
val sectioni : t -> int -> section
sectioni t i returns the i'th section. Raise Failure if no such section.
val sections : t -> section list
Return all sections in t.

Header Information

val data_type : t -> string
Return the type of data, either "signal" or "p-value".
val scale : t -> string
Return scale data is reported in, e.g. linear, log2.
val genomic_map : t -> string
File path of bpmap file used to generate scores.
val alg_name : t -> string
Name of algorithm used to generate scores.
val alg_version : t -> string
Version number of algorithm used.
val coord_convention : t -> string
Probe coordinate convention used.
end