package biocaml

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The OCaml Bioinformatics Library

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biocaml@googlegroups.com

Sources

v0.11.0.tar.gz

md5=486aeb3e552dabae85839e2af30d6c52

sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

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