TAPS_region: Tumor Abberation Prediction Suite - Region plotter

Description Usage Arguments Details Author(s) References

View source: R/TAPS.r

Description

TAPS_region allows you to look closer at a region of the genome that you specify. It also displays the known genes of the region.

Usage

1
TAPS_region(directory=NULL,chr,region,hg18=F)

Arguments

directory

Default is getwd(). Directory must contain TAPS_plot_output.Rdata, an output from TAPS_plot(), which contains all information that TAPS_region() needs.

chr

Supply the chromosome you wish to look at. ex: chr=1

region

The region of the chromosome you are interested in. ex: region=10000000:13000000

hg18

Default is FALSE, meaning the hg19 known gene list will be used. If TRUE the hg18 known gene list is used.

Details

TAPS_region takes the directory of the sample that you want to look at (defaults to current working directory if no input is given), the chromosome and the actual chromosomal coordinates as input to give you an in-depth view. Unlike any of the other plots this view also shows known genes from a gene list of your choice, hg18 or hg19.

Author(s)

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

References

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


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

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