Description Usage Arguments Details Author(s) References
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.
1 | TAPS_estimates(path=getwd())
|
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. |
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().
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.