Description Usage Arguments Value Author(s) Examples
View source: R/facopy_internal_v45.r
The function reads the copy number output generated by one of the supported copy number analysis tools
1 2 |
folder |
A character indicating the path where the files with copy number information are located. In order to avoid possible conflicts, try not to place any additional files within the folder. |
method |
Either |
sex |
Either |
FUN |
A pattern replacement function. Some copy number analysis tools add suffixes and file extension characters to the names of their output files. This function allows keeping just the sample names. Leave to |
version |
A character with the software version of the copy number analysis tool. The output may vary between versions of the same method. Leave to |
window |
An integer. Required for output files from CNAnorm, which do not contain information on the window length used during the copy number analysis process. |
rankThr |
An integer. Threshold on the Rank parameter provided by OncoSNP-SEQ and the newer versions of OncoSNP (>1.3). |
pfbFilename |
For GAP, name of a file with population B allele frequencies (PFB), the same one used during the copy number analysis process. |
lengthThr |
An integer. For GAP, filter those alterations that span less SNPs than this threshold. |
... |
If a method is not selected ( |
A facopyInfo
object with copy number data.
David Mosen-Ansorena
1 2 3 | # myCalls = readCNData("~/myFolder/", "seqcna")
# myCalls = readCNData("~/myFolder/", "gap", pfbFilename="~/myPfb.pfb")
# myCalls = readCNData("~/myFolder/", "cnanorm", window=50000)
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