extract_matchranges {multicrispr} | R Documentation |
Extract subranges that match pattern
extract_matchranges(gr, bsgenome, pattern, plot = FALSE)
gr |
|
bsgenome |
|
pattern |
string: search pattern in extended IUPAC alphabet |
plot |
TRUE or FALSE (default) |
# 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'))