TAPS_compare: Tumor Abberation Prediction Suite

In TAPS: Tumor Abberation Prediction Suite

Description

TAPS_compare generates a comparison of aberration frequencies in two groups of samples (on which TAPS_call has completed).

Usage

TAPS_compare(grp1, grp2, name1='1', name2='2', outdir='frequencies_comp', hg19=T)

Arguments

grp1	Supply a (boolean, integer or sample name) vector of samples in the first group.
grp2	Supply a (boolean, integer or sample name) vector of samples in the second group.
name1	Supply a name for the first group. (Default='1')
name2	Supply a name for the second group. (Default='2')
outdir	All results are written to this directory.
hg19	The reference genome 'hg19' will be used for genes. If FALSE, reverts to hg18.

Details

This function compares aberration frequencies in two groups of samples. Run from the directory containing sample folders. Make sure TAPS_call() completed successfully on all (included) samples.

Author(s)

Markus Mayrhofer, [e-mail]
Hanna Goransson Kultima, [e-mail]
Sebastian DiLorenzo, [e-mail]
Bjorn Viklund, [e-mail]

References

http://www.biomedcentral.com/content/pdf/gb-2011-12-10-r108.pdf

TAPS documentation built on May 2, 2019, 4:47 p.m.