pcaSnpFilters: Regions of SNP-PC correlation to filter for Principal...
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Format Details Source References See Also Examples

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.

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pcaSnpFilters.hg18
pcaSnpFilters.hg19
pcaSnpFilters.hg38

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

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.

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

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

snpCorrelationPlot, SNPRelate

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data(pcaSnpFilters.hg18)
data(pcaSnpFilters.hg19)
data(pcaSnpFilters.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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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