read.CNAT.plain(FASeg) | R Documentation |
This function reads in the plain text output of copy number data from Copy Number Analysis Tool.
read.CNAT.plain(filename)
filename |
The file name of the plain text file. |
When outputing the plain text copy number, please include columns of "_SPA_CN" only or with "_SPA_pVal". Multiple experiment can be output in the same table.
A matrix is returned. The first column is chromosome number; the second is physical location; the third is the SNP-level copy number of the first sample; the fourth the second sample, and so on.
The first row of the file should contain a single item "Copy Number Analysis Tool". If extra tabs are existent, the function will malfunction. Please hand-erase the tabs in a text editor.
Tianwei Yu (tyu8@sph.emory.edu)
SNP.to.cn()