Extract matching subranges

Extract subranges that match pattern

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)
#> GRanges object with 10 ranges and 3 metadata columns:
#>            seqnames              ranges strand |  targetname targetstart
#>               <Rle>           <IRanges>  <Rle> | <character>   <integer>
#>     CFTR_f     chr7 117559575-117559597      + |        CFTR   117559593
#>     CFTR_r     chr7 117559603-117559625      - |        CFTR   117559593
#>      HBB_f    chr11     5226984-5227006      + |         HBB     5227002
#>      HBB_r    chr11     5227000-5227022      - |         HBB     5227002
#>   HEXA_f_1    chr15   72346551-72346573      + |        HEXA    72346580
#>   HEXA_f_2    chr15   72346558-72346580      + |        HEXA    72346580
#>   PRNP_f_1    chr20     4699568-4699590      + |        PRNP     4699600
#>   PRNP_f_2    chr20     4699569-4699591      + |        PRNP     4699600
#>   PRNP_f_3    chr20     4699575-4699597      + |        PRNP     4699600
#>   PRNP_f_4    chr20     4699578-4699600      + |        PRNP     4699600
#>            targetend
#>            <integer>
#>     CFTR_f 117559595
#>     CFTR_r 117559595
#>      HBB_f   5227002
#>      HBB_r   5227002
#>   HEXA_f_1  72346583
#>   HEXA_f_2  72346583
#>   PRNP_f_1   4699600
#>   PRNP_f_2   4699600
#>   PRNP_f_3   4699600
#>   PRNP_f_4   4699600
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome

# 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()
#> 	Read SRF.bed into GRanges
#> 		1974 ranges on 21 chromosomes
extract_matchranges(gr, bsgenome, pattern = strrep('N',20) %>% paste0('NGG'))
#> GRanges object with 6616 ranges and 5 metadata columns:
#>                              seqnames            ranges strand |         name
#>                                 <Rle>         <IRanges>  <Rle> |  <character>
#>     chr1:4712628-4712643:-_5     chr1   4712616-4712638      - | SRF_MA0083.3
#>     chr1:4712628-4712643:-_4     chr1   4712617-4712639      - | SRF_MA0083.3
#>     chr1:4712628-4712643:-_3     chr1   4712624-4712646      - | SRF_MA0083.3
#>     chr1:4712628-4712643:-_2     chr1   4712630-4712652      - | SRF_MA0083.3
#>     chr1:4712628-4712643:-_1     chr1   4712631-4712653      - | SRF_MA0083.3
#>                          ...      ...               ...    ... .          ...
#>   chrY:79048176-79048191:-_2     chrY 79048172-79048194      - | SRF_MA0083.3
#>   chrY:79048176-79048191:-_1     chrY 79048179-79048201      - | SRF_MA0083.3
#>   chrY:89126494-89126509:-_3     chrY 89126489-89126511      - | SRF_MA0083.3
#>   chrY:89126494-89126509:-_2     chrY 89126496-89126518      - | SRF_MA0083.3
#>   chrY:89126494-89126509:-_1     chrY 89126497-89126519      - | SRF_MA0083.3
#>                                  score               targetname targetstart
#>                              <numeric>              <character>   <integer>
#>     chr1:4712628-4712643:-_5   10.4954   chr1:4712628-4712643:-     4712628
#>     chr1:4712628-4712643:-_4   10.4954   chr1:4712628-4712643:-     4712628
#>     chr1:4712628-4712643:-_3   10.4954   chr1:4712628-4712643:-     4712628
#>     chr1:4712628-4712643:-_2   10.4954   chr1:4712628-4712643:-     4712628
#>     chr1:4712628-4712643:-_1   10.4954   chr1:4712628-4712643:-     4712628
#>                          ...       ...                      ...         ...
#>   chrY:79048176-79048191:-_2   9.73780 chrY:79048176-79048191:-    79048176
#>   chrY:79048176-79048191:-_1   9.73780 chrY:79048176-79048191:-    79048176
#>   chrY:89126494-89126509:-_3   4.54393 chrY:89126494-89126509:-    89126494
#>   chrY:89126494-89126509:-_2   4.54393 chrY:89126494-89126509:-    89126494
#>   chrY:89126494-89126509:-_1   4.54393 chrY:89126494-89126509:-    89126494
#>                              targetend
#>                              <integer>
#>     chr1:4712628-4712643:-_5   4712643
#>     chr1:4712628-4712643:-_4   4712643
#>     chr1:4712628-4712643:-_3   4712643
#>     chr1:4712628-4712643:-_2   4712643
#>     chr1:4712628-4712643:-_1   4712643
#>                          ...       ...
#>   chrY:79048176-79048191:-_2  79048191
#>   chrY:79048176-79048191:-_1  79048191
#>   chrY:89126494-89126509:-_3  89126509
#>   chrY:89126494-89126509:-_2  89126509
#>   chrY:89126494-89126509:-_1  89126509
#>   -------
#>   seqinfo: 66 sequences (1 circular) from mm10 genome