Problem in LD-based SNP pruning using SNPRelate

Question

[evelyn]

Hello,

I have an expression data matrix and phenotype data. I started with SNPRelate to get the PCA and IBS analysis using:

library(SNPRelate)
library(gdsfmt)

#Convert vcf file to gds file
vcf.fn <- "data.vcf"
snpgdsVCF2GDS(vcf.fn, "test.gds", method="biallelic.only")
snpgdsSummary("test.gds")

#Data analysis
# Open the GDS file
genofile <- snpgdsOpen("test.gds")
pop_code <- read.gdsn(index.gdsn(genofile, "genotype"))

#LD based SNP pruning
set.seed(1000)
snpset <- snpgdsLDpruning(genofile, autosome.only=FALSE, ld.threshold=0.2)
names(snpset)
head(snpset$ch01)
snpset.id <- unlist(snpset)

#Principal Component Analysis (PCA)
pca <- snpgdsPCA(genofile, autosome.only=FALSE, snp.id=snpset.id, num.thread=2)
pc.percent <- pca$varprop*100
head(round(pc.percent, 2))
tab <- data.framesample.id = pca$sample.id,
    EV1 = pca$eigenvect[,1],    # the first eigenvector
    EV2 = pca$eigenvect[,2],    # the second eigenvector
    stringsAsFactors = FALSE)
head(tab)
plot(tab$EV2, tab$EV1, xlab="eigenvector 2", ylab="eigenvector 1")

#perform the IBS analysis
ibs <- snpgdsIBS(genofile, autosome.only=FALSE, num.thread=2) 
length(ibs$ibs) 
summary(as.vector(ibs$ibs))

set.seed(100)
ibs.hc <- snpgdsHCluster(snpgdsIBS(genofile, autosome.only=FALSE, num.thread=2))
rv <- snpgdsCutTree(ibs.hc)
plot(rv$dendrogram, leaflab="none", main="HapMap Phase II")

snpgdsClose(genofile)

LD-pruning showed some markers were dropped. But PCA and IBS analysis still had the original number of markers. I am not sure what is wrong in the code that the markers based on LD-pruning are not being dropped in further analysis.

Thank you in advance.