read.CNAT.plain(FASeg)R Documentation

A function that reads CNAT plain text output

Description

This function reads in the plain text output of copy number data from Copy Number Analysis Tool.

Usage

read.CNAT.plain(filename)

Arguments

filename The file name of the plain text file.

Details

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.

Value

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.

Note

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.

Author(s)

Tianwei Yu (tyu8@sph.emory.edu)

References

See Also

SNP.to.cn()

Examples






[Package FASeg version 2.0 Index]