find.ip.sites: identify positions of likely internal priming sites by...

In sqjin/nlvelo: RNA velocity estimation using nonlinear models

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')

## End(Not run)

sqjin/nlvelo documentation built on Feb. 11, 2021, 8:09 a.m.