unmasked-datasets {podkat} | R Documentation

## Unmasked Regions of Human Genomes

### Description

Pre-built `GRangesList` objects with unmasked regions of different human genome builds

### Usage

    hg18Unmasked
    hg19Unmasked
    hg38Unmasked
    b36Unmasked
    b37Unmasked

### Format

Each of these is a `GRangesList` object with unmasked regions of different human genome builds, as provided by the packages BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, and BSgenome.Hsapiens.UCSC.hg38.masked. The two latter, `b36Unmasked` and `b37Unmasked`, are variants using chromosome names as the genomes b36 and b37 that are frequently used by the Genome Analysis Toolkit (GATK).

All four data sets comprise all 22 autosomal chromosomes, the two sex chromosomes, mitochondrial DNA, and the six pseudoautosomal regions as defined in the data frames `pseudoautosomal.hg18` (for hg18), `pseudoautosomal.hg19` (for hg19), and `pseudoautosomal.hg38` (for hg38) as provided by the GWASTools package. If this is undesired, the user can re-unite the pseudoautosomal regions with their chromosomes as shown in the example section below or run `unmaskedRegions` him- or herself to extract unmasked regions.

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

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

### See Also

`unmaskedRegions`, `GRangesList`, `GRanges`, `pseudoautosomal`

### Examples

    ## load data sets
    data(hg19Unmasked)
    data(b37Unmasked)

    ## show chromosome names
    seqlevels(hg19Unmasked)
    seqlevels(b37Unmasked)

    ## show names of list components
    names(hg19Unmasked)
    names(b37Unmasked)

    ## determine numbers of regions for each component
    sapply(hg19Unmasked, length)
    sapply(b37Unmasked, length)

    ## re-unite pseudoautosomal regions with their chromosomes
    ## (that is the result of what unmaskedRegions() would have given
    ## without specifying pseudoautosomal regions)
    hg19basic <- hg19Unmasked[paste0("chr", 1:22)]
    hg19basic$chrX <- reduce(unlist(hg19Unmasked[c("chrX", "X.PAR1",
                                                   "X.PAR2", "X.XTR")]))
    hg19basic$chrY <- reduce(unlist(hg19Unmasked[c("chrY", "Y.PAR1",
                                                   "Y.PAR2", "Y.XTR")]))

    ## show some information about the newly created object
    names(hg19basic)
    sapply(hg19basic, length)

[Package podkat version 1.12.0 Index]