extract_matchranges {multicrispr} | R Documentation

## Extract matching subranges

### 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'))

[Package multicrispr version 1.4.3 Index]