R: Transpose genotypic matrix

snpgdsTranspose {SNPRelate}

R Documentation

Transpose genotypic matrix

Description

Transpose the genotypic matrix if needed.

Usage

snpgdsTranspose(gds.fn, snpfirstdim=FALSE, compress=NULL, optimize=TRUE,
    verbose=TRUE)

Arguments

`gds.fn`	the file name of SNP GDS format
`snpfirstdim`	if `TRUE`, genotypes are stored in snp-by-sample; if `FALSE`, sample-by-snp mode; if `NA`, force to transpose the SNP matrix
`compress`	the compression mode for SNP genotypes, optional values are defined in the function of `add.gdsn`; if `NULL`, to use the compression mode
`optimize`	if `TRUE`, call `cleanup.gds` after transposing
`verbose`	if TRUE, show information

Value

None.

Author(s)

Xiuwen Zheng

Examples

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

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

# summary
snpgdsSummary("test.gds")

# transpose the SNP matrix
snpgdsTranspose("test.gds", snpfirstdim=TRUE)

# summary
snpgdsSummary("test.gds")


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

[Package SNPRelate version 1.10.2 Index]