Get intergenic regions

Returns table of intergenic regions for specified genome.

get_intergenic_regions(genome, as_gr = FALSE)

Arguments

genome

Character object specifying the reference genome; accepts one of the following options:

  1. "SK1Yue"

  2. "sacCer3"

  3. "SK1"

No default.
as_gr

Logical specifying whether the output should be returned as a GRanges object. If FALSE, output is a data.frame. Can only be used if genome="SK1Yue", because "SK1" and "sacCer3" contain overlapping genes, resulting in negative intervals (not allowed by IRanges). Defaults to FALSE.

Value

R data frame containing coordinates and annotations for all intergenic regions in the genome.

Examples

# NOT RUN {
get_intergenic_regions(genome='SK1Yue')

get_intergenic_regions(genome='sacCer3')

# }