Check Genomic Regions

A function that takes the users input regions (as '.BED' or GRanges object input) and checks if they are valid genomic regions.

check_region(regions)

Arguments

regions	Input of either a GRanges object or a BED file containing Genomic Regions the user wants to build a RSE object for.

Value

A text output, and if seqlevels(regions) returns a valid output, the regions GRanges object will be returned. The GRanges Object can then be used in the libd_rse function.

Examples

## Define a single example genomic region as GRanges object
genomic_regions <- GenomicRanges::GRanges('chr1:1-100:+')
check_region(genomic_regions)
#> 2019-08-16 12:38:04 The 'regions' selected are valid regions.
#>  Returning regions as a GRanges object.
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1     1-100      +
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

## As BED file input
bed_file <- file.path(tempdir(), 'genomic_regions.bed')
rtracklayer::export.bed(genomic_regions, bed_file)
check_region(bed_file)
#> 2019-08-16 12:38:04 The 'regions' selected are valid regions.
#>  Returning regions as a GRanges object.
#> GRanges object with 1 range and 2 metadata columns:
#>       seqnames    ranges strand |        name     score
#>          <Rle> <IRanges>  <Rle> | <character> <numeric>
#>   [1]     chr1     1-100      + |        <NA>         0
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths