unmaskedRegions {podkat} | R Documentation

## Extract Unmasked Regions from `MaskedBSgenome` Object

### Description

Create a `GRangesList` of unmasked regions from a `MaskedBSgenome` object

### Usage

    unmaskedRegions(x, chrs=character(), pseudoautosomal=NULL,
                    ignoreGaps=250, activeMasks=active(masks(x[[1]])))

### Arguments

`x` | a `MaskedBSgenome` object
`chrs` | a character vector of chromosome names to restrict to; if empty (default), all chromosomes in `x` are considered.
`pseudoautosomal` | if `NULL` (default), the chromosomes are considered as they are; `pseudoautosomal` must be a data frame complying with the format of the `pseudoautosomal.hg18`, `pseudoautosomal.hg19`, and `pseudoautosomal.hg38` from the GWASTools package (see details below).
`ignoreGaps` | skip assembly gaps only if larger than this threshold; in turn, if two unmasked regions are separated by an assembly gap not larger than `ignoreGaps`, they are joined in the resuling `GRanges` object.
`activeMasks` | masks to apply for determining unmasked region; defaults to the masks that are active by default in the `MaskedBSgenome` object `x`. Therefore, this argument only needs to be set if a masking other than the default is necessary.

### Details

This function takes a `MaskedBSgenome` object `x` and extracts the genomic regions that are unmasked in this genome, where the set of masks to apply can be specified using the `activeMasks` argument. The result is returned as a `GRangesList` object each component of which corresponds to one chromosome of the genome `x` - or a subset thereof if the `chrs` argument has been specified.

The `pseudoautosomal` argument allows for a special treatment of pseudoautosomal regions. If not `NULL`, this argument must be a data frame that contains columns with names “chrom”, “start.base”, and “end.base”. The “chrom” column must contain chromosome names as they appear in the `MaskedBSgenome` object `x`. The columns “start.base” and “end.base” must contain numeric values that specify the starts and ends of pseudoautosomal regions, respectively. The function is implemented such that the data frames `pseudoautosomal.hg18`, `pseudoautosomal.hg19`, and `pseudoautosomal.hg38` provided by the GWASTools package can be used (except for the chromosome names that need to be adapted to hg18/hg19/hg38). If the `pseudoautosomal` argument is specified correctly, the `unmaskedRegions` function produces separate components in the resulting `GRangesList` object - one for each pseudoautosomal region. These components are named as the corresponding row names in the data frame `pseudoautosomal`. Moreover, these regions are omitted from the list of unmasked regions of the chromosomes they are on.

### Value

a `GRangesList` object (see details above)

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

http://www.bioinf.jku.at/software/podkat

### See Also

`GRangesList`, `pseudoautosomal`

### Examples

    ## load packages to obtain masked hg38genome and
    ##  pseudoautosomal.hg19 from GWASTools package
    if (require(BSgenome.Hsapiens.UCSC.hg38.masked) && require(GWASTools))
    {
        ## extract unmasked regions of all autosomal chromosomes
        regions <- unmaskedRegions(BSgenome.Hsapiens.UCSC.hg38.masked,
                                   chrs=paste0("chr", 1:22))
        names(regions)
        regions$chr1

        ## adjust chromosome names
        pseudoautosomal.hg38
        psaut <- pseudoautosomal.hg38
        psaut$chrom <- paste0("chr", psaut$chrom)
        psaut

        ## extract unmasked regions of sex chromosomes taking pseudoautosomal
        ## regions into account
        regions <- unmaskedRegions(BSgenome.Hsapiens.UCSC.hg38.masked,
                                   chrs=c("chrX", "chrY"), pseudoautosomal=psaut)
        names(regions)
        regions$chrX
        regions$X.PAR1

        ## check overlap between X chromosome and a pseudoautosomal region
        intersect(regions$chrX, regions$X.PAR1)
    }

[Package podkat version 1.14.0 Index]