velocyto.R (version 0.6)

find.ip.sites: identify positions of likely internal priming sites by looking for polyA/polyT stretches within annotated intronic regions

Description

identify positions of likely internal priming sites by looking for polyA/polyT stretches within annotated intronic regions

Usage

find.ip.sites(gtf.file, genome, genome.name, w = 0.9, n = 15,
  min.score = "80%", add.chr = TRUE)

Arguments

gtf.file

location of a gtf file with gene annotations

genome

bioC genome structure (i.e. Mmusculus)

genome.name

name of the genome assembly (i.e. mm10)

w

A/T weight in the PWM

n

length of the motif

min.score

minimal required match score

add.chr

whether to add 'chr' prefix to the chromosome names in the gtf annotation (to match bioC)

Value

a data frame containing list of likely internal priming sites, listing chromosome ($chr), positions ($start/$end), name, PWM matching score, PWM match strand ($strand), gene, gene strand ($gs), and whether the motif is in concordant direction of gene transcription ($conc)

Examples

# NOT RUN {
library(BSgenome.Mmusculus.UCSC.mm10)
ip.mm10 <- find.ip.sites('refdata-cellranger-mm10-1.2.0/genes/genes.gtf',Mmusculus,'mm10')
# }