Extract subranges

Extract subranges from a GRanges-class object

extract_subranges(gr, ir, plot = FALSE)

Arguments

gr	GRanges-class
ir	IRanges-class: subranges to be extracted
plot	TRUE or FALSE (default)

Value

GRanges-class.

Examples

# Extract a subrange
gr <- GenomicRanges::GRanges(c(A = 'chr1:1-100:+', B = 'chr1:1-100:-'))
gr$targetname <- 'AB'
ir <- IRanges::IRanges(c(A = '1-10', A = '11-20', B = '1-10', B = '11-20'))
extract_subranges(gr, ir, plot = TRUE)
#> GRanges object with 4 ranges and 1 metadata column:
#>       seqnames    ranges strand |  targetname
#>          <Rle> <IRanges>  <Rle> | <character>
#>   A_1     chr1      1-10      + |          AB
#>   A_2     chr1     11-20      + |          AB
#>   B_1     chr1    91-100      - |          AB
#>   B_2     chr1     81-90      - |          AB
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# Return empty GRanges for empty IRanges 
extract_subranges(GenomicRanges::GRanges('chr1:345-456'), IRanges::IRanges())
#> GRanges object with 0 ranges and 0 metadata columns:
#>    seqnames    ranges strand
#>       <Rle> <IRanges>  <Rle>
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths