readNimblegen {Ringo} | R Documentation |
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.
readNimblegen(hybesFile, spotTypesFile, path = getwd(), verbose = TRUE, ...)
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. |
verbose |
logical; progress output to STDOUT? |
... |
further arguments passed on the readNgIntensitiesTxt |
Returns raw intensity values in form of an RGList
.
Joern Toedling toedling@ebi.ac.uk
exDir <- system.file("exData",package="Ringo") exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir) print(exRG)