kin2gds {GENESIS} | R Documentation |
kin2gds
and mat2gds
write kinship matrices to
GDS files.
kin2gds(ibdobj, gdsfile) mat2gds(mat, gdsfile)
ibdobj |
A list with elements |
mat |
A matrix with sample identifiers in colnames. |
gdsfile |
A character string with the name of the GDS file to create. |
When using pcair
or pcairPartition
with large sample sizes, it can be more memory efficient to read data from GDS files. kin2gds
and mat2gds
store kinship matrices in GDS files for use with these functions.
Stephanie M. Gogarten
library(gdsfmt) # KING results from the command-line program file.kin0 <- system.file("extdata", "MXL_ASW.kin0", package="GENESIS") file.kin <- system.file("extdata", "MXL_ASW.kin", package="GENESIS") KINGmat <- kingToMatrix(c(file.kin0, file.kin)) gdsfile <- tempfile() mat2gds(KINGmat, gdsfile) gds <- openfn.gds(gdsfile) gds closefn.gds(gds) # KING results from SNPRelate library(SNPRelate) geno <- snpgdsOpen(snpgdsExampleFileName()) king <- snpgdsIBDKING(geno) closefn.gds(geno) kin2gds(king, gdsfile) gds <- openfn.gds(gdsfile) gds closefn.gds(gds)