README.md

In tinyheero/oncosnputils: Post-processing of OncoSNP Results

oncosnputils - An R package for post-processing the results of OncoSNP

To install this R package, you will need devtools. Then open R and type:

devtools::install_github("tinyheero/oncosnputils", upgrade_dependencies = FALSE)

Overview

The oncosnputils R package main purpose is to supplement some of the output data from OncoSNP. An introduction vignette has been written to describe how to use the R package.

To see the full list of exported functions:

library("oncosnputils")
ls("package:oncosnputils")

For instance, the function add_LRR_BAF_to_oncosnp_cnv functions will add Log R Ratio (LRR) and B-allele frequeny (BAF) information to each CNV segment in the OncoSNP *.cnvs file. Additionally, the add_oncosnp_to_penncnv_probe adds OncoSNP state information to the raw probe data from the PennCNV-Affy protocol. This is useful for plotting the LRR and BAF plots when you want to add colors to the probes.

Also, several loading functions are provided:

• load_oncosnp_qc_file
• load_oncosnp_cnv_file
• load_penncnv_probe_data

These provide quick and easy loading (thanks to data.table::fread) of these tabular OncoSNP output files and PennCNV probe data. Also, the column names will be renamed to help faciliate downstream R analyses.

tinyheero/oncosnputils documentation built on May 31, 2019, 3:36 p.m.