snpgdsGetGeno: To get a genotype matrix

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

Description

To get a genotype matrix from a specified GDS file

Usage

snpgdsGetGeno(gdsobj, sample.id=NULL, snp.id=NULL, snpfirstdim=NA,
    .snpread=NA, with.id=FALSE, verbose=TRUE)

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file; or characters to specify the file name of SNP GDS
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
snpfirstdim	if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc); FALSE for snp-major mode; if NA, determine automatically
.snpread	internal use
with.id	if TRUE, return sample.id and snp.id
verbose	if TRUE, show information

Value

The function returns an integer matrix with values 0, 1, 2 or NA representing the number of reference allele when with.id=FALSE; or list(genotype, sample.id, snp.id) when with.id=TRUE. The orders of sample and SNP IDs in the genotype matrix are actually consistent with sample.id and snp.id in the GDS file, which may not be as the same as the arguments sampel.id and snp.id specified by users.

Author(s)

Xiuwen Zheng

Examples

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

set.seed(1000)
snpset <- sample(read.gdsn(index.gdsn(genofile, "snp.id")), 1000)

mat1 <- snpgdsGetGeno(genofile, snp.id=snpset, snpfirstdim=TRUE)
dim(mat1)
# 1000  279
table(c(mat1), exclude=NULL)

mat2 <- snpgdsGetGeno(genofile, snp.id=snpset, snpfirstdim=FALSE)
dim(mat2)
# 279 1000
table(c(mat2), exclude=NULL)

identical(t(mat1), mat2)
# TRUE

# close the file
snpgdsClose(genofile)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Genotype matrix: 1000 SNPs X 279 samples
[1] 1000  279

     0      1      2   <NA> 
105625  73055  99462    858 
Genotype matrix: 279 samples X 1000 SNPs
[1]  279 1000

     0      1      2   <NA> 
105625  73055  99462    858 
[1] TRUE

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.