snpgdsPCACorr: SNP correlation in principal component analysis

In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description

To calculate the SNP correlations between eigenvactors and SNP genotypes

Usage

snpgdsPCACorr(pcaobj, gdsobj, snp.id=NULL, eig.which=NULL, num.thread=1, verbose=TRUE)

Arguments

pcaobj	the snpgdsPCAClass object returned from the function snpgdsPCA
gdsobj	a GDS file object (gds.class)
snp.id	a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
eig.which	a vector of integers, to specify which eigenvectors to be used
num.thread	the number of CPU cores used
verbose	if TRUE, show information

Value

Return a list:

sample.id	the sample ids used in the analysis
snp.id	the SNP ids used in the analysis
snpcorr	a matrix of correlation coefficients, "# of eigenvectors" x "# of SNPs"

Author(s)

Xiuwen Zheng

References

Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2:e190.

See Also

snpgdsPCA, snpgdsPCASampLoading, snpgdsPCASNPLoading

Examples

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())
# get chromosome index
chr <- read.gdsn(index.gdsn(genofile, "snp.chromosome"))

RV <- snpgdsPCA(genofile)
CORR <- snpgdsPCACorr(RV, genofile, eig.which=1:4)
plot(abs(CORR$snpcorr[3,]), xlab="SNP Index", ylab="PC 3", col=chr)

# close the genotype file
closefn.gds(genofile)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
    using 1 (CPU) core
PCA:    the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Thu Dec  7 09:09:34 2017    (internal increment: 408)

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Thu Dec  7 09:09:34 2017    Begin (eigenvalues and eigenvectors)
Thu Dec  7 09:09:34 2017    Done.
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
SNP Correlation:
Working space: 279 samples, 9088 SNPs
    using 1 (CPU) core
    using the top 4 eigenvectors
Correlation:    the sum of all selected genotypes (0,1,2) = 2553065
Thu Dec  7 09:09:34 2017    (internal increment: 3288)

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Thu Dec  7 09:09:34 2017    Done.

SNPRelate documentation built on May 2, 2019, 4:56 p.m.