package biocaml

You can search for identifiers within the package.

in-package search v0.2.0

The OCaml Bioinformatics Library

Install

Dune Dependency

github.com Readme Edit opam file Versions (5)

Authors

Maintainers

P

philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

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

Module `Biocaml_unix.Cel`Source

Affymetrix's CEL files. Only text format supported. Binary file must be converted using Affymetrix's conversion tool. This tool does not change file extension, so be sure your file really is in text format.

Sourcetype t

The type of a CEL file.

Sourceexception Bad of string

Raised when encountering ill-formed CEL type.

Sourceval of_file : string -> t

Parse given file if possible. Raise Bad if there are any parse errors.

Sourceval of_file_opt : string -> t option

Parse given file if possible.

Operations on Intensity Section

Sourcetype idata = {

mean : float;
(*
mean intensity value
*)
stdv : float;
(*
standard deviation of intensity
*)
npixels : int;
(*
number of pixels used in mean/stdv calculation
*)

}

Sourcetype irow = {

xcoord : int;
(*
x-coordinate
*)
ycoord : int;
(*
y-coordinate
*)
idata : idata;

}

Represents row in intensity section

Sourceval ifold : ('a -> irow -> 'a) -> 'a -> t -> 'a

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

Sourceval iiter : (irow -> unit) -> t -> unit

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

Sourceval data : Bpmap.t -> t list -> (Bpmap.probe * (idata * idata) list) list

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). Raise Failure if any file in cels lacks a value for any probe in bpmap.

Sourceval pm_mm : Bpmap.t -> t list -> (Bpmap.probe * float list) list

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

Sourceval pm : Bpmap.t -> t list -> (Bpmap.probe * float list) list

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

Sourceval mm : Bpmap.t -> t list -> (Bpmap.probe * float list) list

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

On This Page

Operations on Intensity Section