extract_matchranges: Extract matching subranges

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

Description

Extract subranges that match pattern

Usage

extract_matchranges(gr, bsgenome, pattern, plot = FALSE)

Arguments

gr	GRanges-class
bsgenome	BSgenome{BSgenome-class}
pattern	string: search pattern in extended IUPAC alphabet
plot	TRUE or FALSE (default)

Value

GRanges-class

Examples

# PE example
#------------
require(magrittr)
bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38  
gr <- char_to_granges(c(PRNP = 'chr20:4699600:+',             # snp
                        HBB  = 'chr11:5227002:-',             # snp
                        HEXA = 'chr15:72346580-72346583:-',   # del
                        CFTR = 'chr7:117559593-117559595:+'), # ins
                      bsgenome)
gr %<>% extend_for_pe()
pattern <- strrep('N',20) %>% paste0('NGG')
extract_matchranges(gr, bsgenome, pattern, plot = TRUE)

# TFBS examples
#--------------
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
bedfile  <- system.file('extdata/SRF.bed', package='multicrispr')
gr <- bed_to_granges(bedfile, 'mm10') %>% extend()
extract_matchranges(gr, bsgenome, pattern = strrep('N',20) %>% paste0('NGG'))

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.