pcaSnpFilters {GWASTools} | R Documentation

## 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)

[Package GWASTools version 1.38.0 Index]