| snpgdsAlleleSwitch {SNPRelate} | R Documentation |
Switch alleles according to the reference if needed.
snpgdsAlleleSwitch(gdsobj, A.allele, verbose=TRUE)
gdsobj |
an object of class |
A.allele |
characters, referring to A allele |
verbose |
if TRUE, show information |
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.
Xiuwen Zheng
# 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)