readNimblegen {Ringo}R Documentation

Function to read in Nimblegen Intensity Text Files

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(), 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 the files hybesFile and spotTypesFile and also the intensity files.
verbose logical; progress output to STDOUT?
... futher arguments passed on the readNgIntensitiesTxt

Value

Returns raw intensity values in form of an RGList.

Author(s)

Joern Toedling toedling@ebi.ac.uk

See Also

rglist, readTargets

Examples

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

[Package Ringo version 1.0.0 Index]