R: SNP loadings in principal component analysis

snpgdsPCASNPLoading {SNPRelate}

R Documentation

SNP loadings in principal component analysis

Description

To calculate the SNP loadings in Principal Component Analysis

Usage

snpgdsPCASNPLoading(pcaobj, gdsobj, num.thread=1L, verbose=TRUE)

Arguments

`pcaobj`	a `snpgdsPCAClass` object returned from the function snpgdsPCA or a `snpgdsEigMixClass` from snpgdsEIGMIX
`gdsobj`	an object of class `SNPGDSFileClass`, a SNP GDS file
`num.thread`	the number of (CPU) cores used; if `NA`, detect the number of cores automatically
`verbose`	if TRUE, show information

Details

Calculate the SNP loadings (or SNP eigenvectors) from the principal component analysis conducted in snpgdsPCA.

Value

Returns a snpgdsPCASNPLoading object if pcaobj is snpgdsPCAClass, which is a list:

`sample.id`	the sample ids used in the analysis
`snp.id`	the SNP ids used in the analysis
`eigenval`	eigenvalues
`snploading`	SNP loadings, or SNP eigenvectors
`TraceXTX`	the trace of the genetic covariance matrix
`Bayesian`	whether use bayerisan normalization
`avgfreq`	two times allele frequency used in `snpgdsPCA`
`scale`	internal parameter

Or returns a snpgdsEigMixSNPLoadingClass object if pcaobj is snpgdsEigMixClass, which is a list:

`sample.id`	the sample ids used in the analysis
`snp.id`	the SNP ids used in the analysis
`eigenval`	eigenvalues
`snploading`	SNP loadings, or SNP eigenvectors
`afreq`	allele frequency

Author(s)

Xiuwen Zheng

References

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

Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 38, 904-909.

Zhu, X., Li, S., Cooper, R. S., and Elston, R. C. (2008). A unified association analysis approach for family and unrelated samples correcting for stratification. Am J Hum Genet, 82(2), 352-365.

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

PCARV <- snpgdsPCA(genofile, eigen.cnt=8)
SnpLoad <- snpgdsPCASNPLoading(PCARV, genofile)

names(SnpLoad)
# [1] "sample.id"  "snp.id"     "eigenval"   "snploading" "TraceXTX"
# [6] "Bayesian"   "avgfreq"    "scale"
dim(SnpLoad$snploading)
# [1]     8 8722

plot(SnpLoad$snploading[1,], type="h", ylab="PC 1")

# close the genotype file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]