snpgdsDiss: Individual dissimilarity analysis

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

Description

Calculate the individual dissimilarities for each pair of individuals

Usage

snpgdsDiss(gdsobj, sample.id=NULL, snp.id=NULL, autosome.only=TRUE,
	remove.monosnp=TRUE, maf=NaN, missing.rate=NaN, num.thread=1, verbose=TRUE)

Arguments

gdsobj	a GDS file object (gds.class)
sample.id	a vector of sample id specifying selected samples; if NULL, all samples are used
snp.id	a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
autosome.only	if TRUE, use autosomal SNPs only
remove.monosnp	if TRUE, remove monomorphic SNPs
maf	to use the SNPs with ">= maf" only; if NaN, no MAF threshold
missing.rate	to use the SNPs with "<= missing.rate" only; if NaN, no missing threshold
num.thread	the number of CPU cores used
verbose	if TRUE, show information

Details

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

The details will be described in future.

Value

Return a class "snpgdsDissClass":

sample.id	the sample ids used in the analysis
snp.id	the SNP ids used in the analysis
diss	a matrix of individual dissimilarity

Author(s)

Xiuwen Zheng

See Also

snpgdsHCluster

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