snpgdsAdmixProp: Estimate ancestral proportions from the eigen-analysis

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

Estimate ancestral proportions from the eigen-analysis

Description

Estimate ancestral (admixture) proportions based on the eigen-analysis.

Usage

snpgdsAdmixProp(eigobj, groups, bound=FALSE)

Arguments

eigobj	an object of snpgdsEigMixClass from snpgdsEIGMIX, or an object of snpgdsPCAClass from snpgdsPCA
groups	a list of sample IDs, such like groups = list( CEU = c("NA0101", "NA1022", ...), YRI = c("NAxxxx", ...), Asia = c("NA1234", ...))
bound	if TRUE, the estimates are bounded in [0, 1], and the sum of proportions is one; bound=FALSE for unbiased estimates

Details

The minor allele frequency and missing rate for each SNP passed in snp.id are calculated over all the samples in sample.id.

Value

Return a matrix of ancestral proportions with rows for study individuals (rownames() is sample ID).

Author(s)

Xiuwen Zheng

References

Zheng X, Weir BS. Eigenanalysis on SNP Data with an Interpretation of Identity by Descent. Theoretical Population Biology. 2015 Oct 23. pii: S0040-5809(15)00089-1. doi: 10.1016/j.tpb.2015.09.004. [Epub ahead of print]

See Also

snpgdsEIGMIX, snpgdsPCA, snpgdsAdmixPlot

Examples

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

# get population information
#   or pop_code <- scan("pop.txt", what=character())
#   if it is stored in a text file "pop.txt"
pop_code <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))

# get sample id
samp.id <- read.gdsn(index.gdsn(genofile, "sample.id"))

# run eigen-analysis
RV <- snpgdsEIGMIX(genofile)

# eigenvalues
RV$eigenval

# make a data.frame
tab <- data.frame(sample.id = samp.id, pop = factor(pop_code),
    EV1 = RV$eigenvect[,1],    # the first eigenvector
    EV2 = RV$eigenvect[,2],    # the second eigenvector
    stringsAsFactors = FALSE)
head(tab)

# draw
plot(tab$EV2, tab$EV1, col=as.integer(tab$pop),
    xlab="eigenvector 2", ylab="eigenvector 1")
legend("bottomleft", legend=levels(tab$pop), pch="o", col=1:4)


# define groups
groups <- list(CEU = samp.id[pop_code == "CEU"],
    YRI = samp.id[pop_code == "YRI"],
    CHB = samp.id[is.element(pop_code, c("HCB", "JPT"))])

prop <- snpgdsAdmixProp(RV, groups=groups)
head(prop)

# draw
plot(prop[, "YRI"], prop[, "CEU"], col=as.integer(tab$pop),
    xlab = "Admixture Proportion from YRI",
    ylab = "Admixture Proportion from CEU")
abline(v=0, col="gray25", lty=2)
abline(h=0, col="gray25", lty=2)
abline(a=1, b=-1, col="gray25", lty=2)
legend("topright", legend=levels(tab$pop), pch="o", col=1:4)


# draw
snpgdsAdmixPlot(prop, group=pop_code)


# close the genotype file
snpgdsClose(genofile)

zhengxwen/SNPRelate documentation built on April 16, 2024, 8:42 a.m.