Pseudoautosomal region base positions

Description

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

Usage

pseudoautosomal.hg18
pseudoautosomal.hg19
pseudoautosomal.hg38

Format

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

Details

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

Source

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/).

References

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.

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GWASTools)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/pseudoautosomal.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pseudoautosomal
> ### Title: Pseudoautosomal region base positions
> ### Aliases: pseudoautosomal pseudoautosomal.hg18 pseudoautosomal.hg19
> ###   pseudoautosomal.hg38
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(pseudoautosomal.hg18)
> data(pseudoautosomal.hg19)
> data(pseudoautosomal.hg38)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>