TAPS_call: Tumor Abberation Prediction Suite

In TAPS: Tumor Abberation Prediction Suite

Description

TAPS_call calculates genome-wide total and minor copynumbers of tumor samples.

Usage

TAPS_call(samples='all',directory=getwd(),cores=1)

Arguments

samples	Default is 'all'. Alternatively, supply a (boolean, integer or sample name) vector of included samples.
directory	Directory where the sample folders reside. Default is current directory.
cores	Default is 1. Only supported on unix based systems. Set amount of threads/cores to be used.

Details

TAPS_call is the second step in the TAPS analysis, to be run after TAPS_plot. It requires:
1) Your interpretation of plots which you add to the SampleData.csv file:
cn1-cn3: The log-ratio of copy number 1-3 (in the main clone), any two or three of these values are required.
loh: The allelic imbalance of copy number 2 LOH.
(Default values are fine for fairly pure, near-diploid samples)
See website for further instructions: http://patchwork.r-forge.r-project.org/
2) The .Rdata files previously generated by TAPS_plot().

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.