package biocaml

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The OCaml Bioinformatics Library

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Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

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biocaml@googlegroups.com

Sources

v0.10.1.tar.gz

md5=4cf944bcae5d36bf47b67f6bcb2455d7

sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

doc/biocaml.unix/Biocaml_unix/Bar/index.html

Module `Biocaml_unix.Bar`

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.

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.

val num_sections : t -> int

Returns the number of 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.

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Header Information