GRanges <-> data.table

GRanges <-> data.table

gr2dt(gr)

dt2gr(dt, seqinfo)

Arguments

gr	GRanges-class
dt	data.table
seqinfo	Seqinfo-class

Value

data.table (gr2dt) or GRanges (dt2gr)

Examples

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)
(dt <- gr2dt(gr))
#>    seqnames     start       end width strand targetname targetstart targetend
#> 1:    chr20   4699600   4699600     1      +       PRNP     4699600   4699600
#> 2:    chr11   5227002   5227002     1      -        HBB     5227002   5227002
#> 3:    chr15  72346580  72346583     4      -       HEXA    72346580  72346583
#> 4:     chr7 117559593 117559595     3      +       CFTR   117559593 117559595
#>    names
#> 1:  PRNP
#> 2:   HBB
#> 3:  HEXA
#> 4:  CFTR
(gr <- dt2gr(dt, BSgenome::seqinfo(bsgenome)))
#> GRanges object with 4 ranges and 3 metadata columns:
#>        seqnames              ranges strand |  targetname targetstart targetend
#>           <Rle>           <IRanges>  <Rle> | <character>   <integer> <integer>
#>   PRNP    chr20             4699600      + |        PRNP     4699600   4699600
#>    HBB    chr11             5227002      - |         HBB     5227002   5227002
#>   HEXA    chr15   72346580-72346583      - |        HEXA    72346580  72346583
#>   CFTR     chr7 117559593-117559595      + |        CFTR   117559593 117559595
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome