TAPS_estimates: Tumor Aberration Prediction Suite - Estimate allele-specific...

In TAPS: Tumor Abberation Prediction Suite

Description

TAPS_estimates() is intended to be used after TAPS_plot() and before TAPS_click().

TAPS_estimates() estimates the samples allele-specific copynumbers and loss of heterozygosity occurence.

Usage

TAPS_estimates(path=getwd())

Arguments

path

Default is getwd(). Specifying to a specific samples directory will run TAPS_estimates on that directory. Specifying a directory containing one or more subdirectories that are samples (and not any other subdirectories or TAPS_estimates will error when trying to run them!) will iteratively run TAPS_estimates on all samples.

Details

TAPS_estimates() automatically loads shortRegions.Rdata and attempts to estimate the allele-specific copynumbers. Note that it does not always do this correctly. As such it should be used primarily to simplify TAPS_plot output interpretation but should not be used INSTEAD OF TAPS_click().

For example:
1. Run TAPS_plot().
2. Run TAPS_estimates().
3. Run TAPS_click(), some of the estimates made by TAPS_estimates are good and we can accept them, some are bad and we choose to redo them.
4. Run TAPS_call().

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.