snpgdsAlleleSwitch: Allele-switching

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

Description

Switch alleles according to the reference if needed.

Usage

snpgdsAlleleSwitch(gdsobj, A.allele, verbose=TRUE)

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file
A.allele	characters, referring to A allele
verbose	if TRUE, show information

Value

A logical vector with TRUE indicating allele-switching and NA when it is unable to determine. NA occurs when A.allele = NA or A.allele is not in the list of alleles.

Author(s)

Xiuwen Zheng

Examples

# the file name of SNP GDS
(fn <- snpgdsExampleFileName())

# copy the file
file.copy(fn, "test.gds", overwrite=TRUE)

# open the SNP GDS file
genofile <- snpgdsOpen("test.gds", readonly=FALSE)

# allelic information
allele <- read.gdsn(index.gdsn(genofile, "snp.allele"))
allele.list <- strsplit(allele, "/")

A.allele <- sapply(allele.list, function(x) { x[1] })
B.allele <- sapply(allele.list, function(x) { x[2] })

set.seed(1000)
flag <- rep(FALSE, length(A.allele))
flag[sample.int(length(A.allele), 50, replace=TRUE)] <- TRUE

A.allele[flag] <- B.allele[flag]
A.allele[sample.int(length(A.allele), 10, replace=TRUE)] <- NA
table(A.allele, exclude=NULL)


# allele switching
z <- snpgdsAlleleSwitch(genofile, A.allele)

table(z, exclude=NULL)


# close the file
snpgdsClose(genofile)


# delete the temporary file
unlink("test.gds", force=TRUE)

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