pseudoautosomal: Pseudoautosomal region base positions
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Format Details Source References Examples

Pseudoautosomal region (XTR, PAR1, PAR2) base positions for the X and Y chromsosomes from the GRCh36/hg18, GRCh37/hg19 and GRCh38/hg38 genome builds.

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pseudoautosomal.hg18
pseudoautosomal.hg19
pseudoautosomal.hg38

A data.frame with the following columns.

chrom: chromosome (X or Y)
region: region (XTR, PAR1, or PAR2)
start.base: starting base position of region
end.base: ending base position of region

The XTR region on X is defined as DXS1217 to DXS3. The XTR region on Y is defined as SY20 to DXYS1.

hg18 and hg19: UCSC genome browser (http://genome.ucsc.edu)

hg38: Genome Reference Consortium (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/).

Ross, Mark. T. et al. (2005), The DNA sequence of the human X chromosome. Nature, 434: 325-337. doi:10.1038/nature03440

Mumm, S., Molini, B., Terrell, J., Srivastava, A., and Schlessinger, D. (1997), Evolutionary features of the 4-Mb Xq21.3 XY homology region revealed by a map at 60-kb resolution. Genome Res. 7: 307-314.

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data(pseudoautosomal.hg18)
data(pseudoautosomal.hg19)
data(pseudoautosomal.hg38)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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