README.md

In Bio-Core/BioCore.Annotation: BioCore Variant Annotation Package

BioCore.Annotation

A R package for handling postprocessing of data generated by the Bio-Core team at the Princess Margaret Cancer Centre.

Installation

The R package can be installed from GitHub using the "devtools" library inside the R console.

library(devtools)
install_github("bio-core/BioCore.Annotation")

Installation of Dependencies

There are several library/package dependencies that are required before the BioCore.Annotation can be used. The following provides a list of packages and how to install them using the R console.

install.packages("plyr")
install.packages("dplyr")
install.packages("deconstructSigs")
install_github("rdeborja/plotting.general")

To install Biostrings, refer to the BioConductor package page.

Exported functions

The following functions are exported from the package.

• create_recurrence_table
• create_recurrence_heatmap
• create_variant_signature_barplot
• filter_on_depth
• filter_on_population
• get_annovar_files
• get_coding_mutations
• get_snv

Bio-Core/BioCore.Annotation documentation built on Feb. 3, 2020, 6:01 p.m.