readNimblegen: Function to read in Nimblegen Intensity Text Files

In Ringo: R Investigation of ChIP-chip Oligoarrays

Description

Function to read in Nimblegen Intensity Text Files into an RGList. Calls some other functions for actual reading of data. This function is to be used with two-color NimbleGen array data. Use the function read.xysfiles of the oligo package for single-color data.

Usage

readNimblegen(hybesFile, spotTypesFile, path = getwd(),
 headerPattern="# software=NimbleScan",verbose = TRUE, ...)

Arguments

hybesFile	Name of the file describing the arrays. In limma this file would be called targets file.
spotTypesFile	spot types also used by limma
path	Path to directoy that hold the files hybesFile, spotTypesFile and also the intensity files. Set this to NULL if you prefer the arguments hybesFile, spotTypesFile and the file-name entries of the hybes file to be treated as absolute or relative file paths themselves.
headerPattern	string; pattern used to identify explantory header lines in the supplied pair-format files
verbose	logical; progress output to STDOUT?
...	further arguments passed on the readNgIntensitiesTxt

Value

Returns raw intensity values in form of an RGList.

Author(s)

Joern Toedling

See Also

rglist, readTargets

Examples

  exDir <- system.file("exData",package="Ringo")
  exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
  print(exRG)

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.