geneFactors: Returns a factor vector across pos (chr:pos vector)...

In JEFworks/badger: Bayesian approach for detecting copy number alterations from single cell RNA-seq data

Description

Returns a factor vector across pos (chr:pos vector) indicating if the pos is in one of the genes (row number)

Usage

geneFactors(posList, gtf, fill = TRUE, gene = TRUE)

Arguments

posList	Data frame of SNP positions
gtf	GTF file contents
fill	Boolean of whether to map SNPs not annotated as within genes to unique gene ids
gene	Boolean of whether to use genes (or exons only)

Value

a factor vector across pos (chr:pos vector) indicating if the pos is in one of the genes (row number)

Examples

posList <- data.frame(
    'chr' = c('1', '1', '1', '2', '2', '3'),
    'pos' = c(11869+7, 11869+100, 14363+101, 29554+0, 52473+10, 62948+5)
    )
## Not run: 
gtfFile <- 'Homo_sapiens.GRCh37.75.gtf'
gtf <- read.table(gtfFile, header=F, stringsAsFactors=F, sep='\t')
geneFactors(posList, gtf)

## End(Not run)

JEFworks/badger documentation built on May 7, 2019, 7:40 a.m.