To install this R package, you will need devtools. Then open R and type:
devtools::install_github("tinyheero/oncosnputils", upgrade_dependencies = FALSE)
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:
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:
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.
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