package biocaml

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The OCaml Bioinformatics Library

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Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

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biocaml@googlegroups.com

Sources

v0.10.1.tar.gz

md5=4cf944bcae5d36bf47b67f6bcb2455d7

sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

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

Module `Biocaml_unix.Cel`

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.

type t

The type of a CEL file.

exception Bad of string

Raised when encountering ill-formed CEL type.

val of_file : string -> t

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

val of_file_opt : string -> t option

Parse given file if possible.

Operations on Intensity Section

type idata = {

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

}

type irow = {

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

}

Represents row in intensity section

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

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

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

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

val 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.

val 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.

val 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.

val 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