package biocaml

  1. Overview
  2. Docs
package biocaml
Legend:
Page
Library
Module
Module type
Parameter
Class
Class type
Source

Module Biocaml_unix.CelSource

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 = {
  1. mean : float;
    (*

    mean intensity value

    *)
  2. stdv : float;
    (*

    standard deviation of intensity

    *)
  3. npixels : int;
    (*

    number of pixels used in mean/stdv calculation

    *)
}
Sourcetype irow = {
  1. xcoord : int;
    (*

    x-coordinate

    *)
  2. ycoord : int;
    (*

    y-coordinate

    *)
  3. 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.

OCaml

Innovation. Community. Security.

GitHub Discord Twitter Peertube RSS
About
Changelog Releases Industrial Users Academic Users Why OCaml
Ecosystem
Packages Community Events OCaml Planet Jobs
Resources
Install OCaml Get Started Platform Tools Language Manual Standard Library API Books Exercises Papers OCaml Playground Logo
Policies
Carbon Footprint Governance Privacy Code of Conduct