snpgdsPCASNPLoading: SNP loadings in principal component analysis

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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.

See Also

snpgdsPCA, snpgdsEIGMIX, snpgdsPCASampLoading, snpgdsPCACorr

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)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.