Description Usage Arguments Details Author(s) References
TAPS_call calculates genome-wide total and minor copynumbers of tumor samples.
1 |
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. |
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().
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se
Hanna Goransson Kultima, hanna.goransson.kultima@medsci.uu.se
Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
Bjorn Viklund, bjorn.viklund@medsci.uu.se
http://www.biomedcentral.com/content/pdf/gb-2011-12-10-r108.pdf
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