unmasked-datasets: Unmasked Regions of Human Genomes

In podkat: Position-Dependent Kernel Association Test

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 [e-mail]

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)

podkat documentation built on Nov. 8, 2020, 6:55 p.m.