readAgilent {rCGH} | R Documentation |
"rCGH-Agilent"
Constructor.
A constructor function taking as input an Agilent FE .txt file, exported from
Feature Extraction, possibly in a compressed format (.bz2 or .gz).
Agilent from 44 to 400K are supported.
readAgilent(filePath, sampleName = NA, labName = NA, supFlags = TRUE, genome = c("hg19", "hg18", "hg38"), ploidy = 2, verbose = TRUE)
filePath |
: string. A path to an Agilent FE (.txt) file. |
sampleName |
: string. A sample Id. Optional. |
labName |
: string. A lab Id. Optional. |
supFlags |
: should the flagged probes be suppressed. Default is |
genome |
: string. The genome build to use. Supported genomes are |
ploidy |
: numeric. A priori ploidy value, when known, to adjust the estimation of copy numbers. Default is 2. |
verbose |
: logical. if |
When available in the file preambule, several array information will be stored
in Object@info
: scanning date, grid version,...
Any other useful item can be stored using setInfo
.
An object of class "rCGH"
Frederic Commo
readAffyCytoScan
, readAffySNP6
,
readGeneric
, readAffyOncoScan
,
setInfo
, getInfo
filePath <- system.file("extdata", "Agilent4x180K.txt.bz2", package = "rCGH") cgh <- readAgilent(filePath, sampleName = "Agilent4x180K", labName = "myLab") cgh