unmasked-datasets | R Documentation |
Pre-built GRangesList
objects with
unmasked regions of different human genome builds
hg18Unmasked hg19Unmasked hg38Unmasked b36Unmasked b37Unmasked
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.
Ulrich Bodenhofer bodenhofer@bioinf.jku.at
http://www.bioinf.jku.at/software/podkat
unmaskedRegions
, GRangesList
,
GRanges
,
pseudoautosomal
## 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)
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