Regions of SNP-PC correlation to filter for Principal Component Analysis

Description

Base positions for the LCT (2q21), HLA (including MHC), and inversion (8p23, 17q21.31) regions from the GRCh36/hg18, GRCh37/hg19 and GRCh38/hg38 genome genome builds.

Usage

pcaSnpFilters.hg18
pcaSnpFilters.hg19
pcaSnpFilters.hg38

Format

A data.frame with the following columns.

chrom

chromsome

start.base

starting base position of region

end.base

ending base position of region

comment

description of the region

Details

These regions result in high SNP-PC correlation if they are included in Principal Component Analysis (PCA). The pcaSnpFilters datasets can be used to filter SNPs prior to running PCA to avoid correlations.

Source

UCSC genome browser (http://genome.ucsc.edu).

References

Novembre, John et al. (2008), Genes mirror geography within Europe. Nature, 456: 98-101. doi:10.1038/nature07331

See Also

snpCorrelationPlot, SNPRelate

Examples

data(pcaSnpFilters.hg18)
data(pcaSnpFilters.hg19)
data(pcaSnpFilters.hg38)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/pcaSnpFilters.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pcaSnpFilters
> ### Title: Regions of SNP-PC correlation to filter for Principal Component
> ###   Analysis
> ### Aliases: pcaSnpFilters pcaSnpFilters.hg18 pcaSnpFilters.hg19
> ###   pcaSnpFilters.hg38
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(pcaSnpFilters.hg18)
> data(pcaSnpFilters.hg19)
> data(pcaSnpFilters.hg38)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>