Find GG

Find GG

find_gg(gr)

Arguments

gr	GRanges-class

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_pe_to_gg(plot = TRUE) %>% add_seq(bsgenome)
    find_gg(gr)
#> GRanges object with 10 ranges and 3 metadata columns:
#>        seqnames              ranges strand |  targetname targetstart targetend
#>           <Rle>           <IRanges>  <Rle> | <character>   <integer> <integer>
#>    [1]     chr7 117559596-117559597      + |        CFTR   117559593 117559595
#>    [2]     chr7 117559603-117559604      - |        CFTR   117559593 117559595
#>    [3]    chr11     5227000-5227001      - |         HBB     5227002   5227002
#>    [4]    chr11     5227005-5227006      + |         HBB     5227002   5227002
#>    [5]    chr15   72346572-72346573      + |        HEXA    72346580  72346583
#>    [6]    chr15   72346579-72346580      + |        HEXA    72346580  72346583
#>    [7]    chr20     4699589-4699590      + |        PRNP     4699600   4699600
#>    [8]    chr20     4699590-4699591      + |        PRNP     4699600   4699600
#>    [9]    chr20     4699596-4699597      + |        PRNP     4699600   4699600
#>   [10]    chr20     4699599-4699600      + |        PRNP     4699600   4699600
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome