Write GRanges to file

Write GRanges to file

write_ranges(gr, file, verbose = TRUE)

read_ranges(file, bsgenome)

Arguments

gr	GRanges-class
file	file
verbose	TRUE (default) or FALSE
bsgenome	BSgenome-class

Value

GRanges-class for read_ranges

Examples

# Find PE spacers for 4 clinically relevant loci (Anzalone et al, 2019)
    bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
    gr <- char_to_granges(c(
        PRNP = 'chr20:4699600:+',             # snp: prion disease
        HBB  = 'chr11:5227002:-',             # snp: sickle cell anemia
        HEXA = 'chr15:72346580-72346583:-',   # del: tay sachs disease
        CFTR = 'chr7:117559593-117559595:+'), # ins: cystic fibrosis
        bsgenome)
    file <- file.path(tempdir(), 'gr.txt')
    write_ranges(gr, file)
#> Write to C:\Users\abhagwa\AppData\Local\Temp\Rtmp0ApPOT/gr.txt
    read_ranges(file, 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