annotateSegments: cnTools: annotate GRanges segments

In quevedor2/CCLid: Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets

Description

cnTools: annotate GRanges segments

Usage

annotateSegments(
  cn.data,
  genes,
  out.key = "SYMBOL",
  mart = NULL,
  use.mart = FALSE
)

Arguments

cn.data	[Data.frame]: A dataframe that can be converted to GRanges object easily, or a granges object
genes	[GRanges]: A GRanges object of genes with gene_ids housing annotation data. Easiest as the output from getGenes()
out.key	Gene out.key, default is SYMBOL
mart	[object]: A biomart object if you want to annotate missed genes with ensembl
use.mart	[boolean]: If no mart is given, it will load in a biomart object

Value

Annotated GRanges object with gene ids for the input GRanges

quevedor2/CCLid documentation built on July 15, 2020, 4:05 a.m.