Description Usage Arguments Details Value Author(s) Examples
Extract copy-number signals from aroma files. It requires to have executed the normalization process suggested by aroma packages, by using signalPreProcess for example.
1 2 3 4 5 6 7 8 | getCopyNumberSignal(
dataSetName,
chromosome,
normalTumorArray,
onlySNP = FALSE,
listOfFiles = NULL,
verbose = TRUE
)
|
dataSetName |
The name of the data-set folder (it must correspond to a folder name in rawData folder.). |
chromosome |
A vector containing the chromosomes for which the signal will be extracted. |
normalTumorArray |
Only in the case of normal-tumor study. A csv file or a data.frame containing the mapping between normal and tumor files. The first column contains the name of normal files and the second the names of associated tumor files. |
onlySNP |
If TRUE, only the copy-number for SNPs positions will be returned (default=FALSE). |
listOfFiles |
A vector containing the names of the files in dataSetName folder for which the copy-number profiles will be extracted (default is all the files). |
verbose |
If TRUE print some information (default=TRUE). |
The aroma architecture must be respected. The working directory must contain rawData folder and totalAndFracBData folder. To easily access the names of the files available in a dataset, one can use the getListOfFiles function.
a list of length the number of chromosomes containing a data.frame with columns:
Chromosome of the signal.
Positions associated with the copy-number.
Copy number profiles of selected files; the name of each column is the name of the associated data file name.
Names of the probes.
Quentin Grimonprez
1 2 3 4 5 6 | ## Not run:
#DO NOT EXECUTE before reading the vignette
C=getCopyNumberSignal("data1",5,normalTumorArray,TRUE)
C=getCopyNumberSignal("data2",5,onlySNP=TRUE)
## End(Not run)
|
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