README.md

In tinyheero/titanCNAutils: An R package for working with TitanCNA Results

titanCNAutils

An R package for working with TitanCNA results.

Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L. M., et al. (2014). TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res, 24(11), 1881–1893. http://doi.org/10.1101/gr.180281.114

As this is not part of Bioconductor yet, you will need to manually install some Bioconductor packages first:

source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
biocLite("S4Vectors")
biocLite("IRanges")

Once these Bioconductor packages are installed, you can install this package using devtools:

devtools::install_github("tinyheero/titanCNAutils")

Overview

To see the full list of exported functions:

library("titanCNAutils")
ls("package:titanCNAutils")

A quick overview of some of the key functions:

• load_titan_seg(): Loads a TitanCNA segment file generated from the createTITANsegmentfiles.pl script
• get_overlap_seg_with_mask_ind(): Identify TitanCNA segments that overlap with potential germline CNV segments
• get_gene_titan_seg_overlap(): Annotates the TitanCNA segments with gene annotations

tinyheero/titanCNAutils documentation built on May 31, 2019, 3:37 p.m.