package biocaml

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The OCaml Bioinformatics Library

Install 

dune-project
 Dependency

github.com Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. P
    philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz
sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d
sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

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

Module Biocaml_unix.BarSource

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.

Sourcetype t

Type of a BAR file, which can be thought of as a header plus set of sections.

Sourceexception Bad of string
Sourcetype section = private {
  1. sec_num : int;
    (*

    order in which section appears in file, first section is numbered 1

    *)
  2. sec_name : string;
    (*

    chromosome name relative to which coordinates are given

    *)
  3. sec_data : (int * float) list;
    (*

    pairs of coordinate-score data

    *)
}
Sourceval of_file : string -> t

Parse file. Raise Bad if there are parse errors.

Sourceval 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).

Sourceval section : t -> string -> section

section t name returns the section named name. Raise Failure if no such section.

Sourceval sectioni : t -> int -> section

sectioni t i returns the i'th section. Raise Failure if no such section.

Sourceval sections : t -> section list

Return all sections in t.

Sourceval num_sections : t -> int

Returns the number of sections in t

Header Information
Sourceval data_type : t -> string

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

Sourceval scale : t -> string

Return scale data is reported in, e.g. linear, log2.

Sourceval genomic_map : t -> string

File path of bpmap file used to generate scores.

Sourceval alg_name : t -> string

Name of algorithm used to generate scores.

Sourceval alg_version : t -> string

Version number of algorithm used.

Sourceval coord_convention : t -> string

Probe coordinate convention used.