readAffyOncoScan {rCGH} | R Documentation |
"rCGH-oncoScan"
ConstructorA constructor function which takes an Affymetrix oncoScan tabulated
file as input, possibly in a compressed format (.bz2 or .gz).
This can be either a 'ProbeSets,CopyNumber.tsv'
alone, or merged with its
corresponding 'ProbeSets,AllelicData.tsv'
file. See the details
section.
readAffyOncoScan(filePath, sampleName=NA, labName=NA, genome = c("hg19", "hg18", "hg38"), ploidy = 2, verbose=TRUE)
filePath |
: string. A path to an Affymetrix .tsv file. See |
sampleName |
: string. A sample Id. Optional. |
labName |
: string. A lab Id. Optional. |
genome |
: string. The genome build to use. Supported genomes are |
ploidy |
: numeric. A priori plody value, when known, to adjust the estimation of copy numbers. Default is 2. |
verbose |
: logical. When |
The Affymetrix Power Tools apt-copynumber-onco-ssa
script produces 2
files: 'ProbeSets,CopyNumber.tsv'
and 'ProbeSets,AllelicData.tsv'
.
Merging these 2 files may produce a unique file containing both probes
Log2Ratio
and AllelicDifference
.
An object of class "rCGH"
Frederic Commo
readAgilent
, readAffySNP6
,
readGeneric
, readAffyCytoScan
,
setInfo
, getInfo
# Just a toy file filePath <- system.file("extdata", "oncoscan.tsv.bz2", package = "rCGH") cgh <- readAffyOncoScan(filePath, sampleName = "AffyOncoScan") cgh