Module Biocaml.Bar (.ml)

module Bar: Biocaml_bar

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.