Description Usage Arguments Value Examples
View source: R/momentum_routines.R
identify positions of likely internal priming sites by looking for polyA/polyT stretches within annotated intronic regions
1 2 | find.ip.sites(gtf.file, genome, genome.name, w = 0.9, n = 15,
min.score = "80%", add.chr = TRUE)
|
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) |
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)
1 2 3 4 5 | ## 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)
|
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