| snpgdsPED2GDS {SNPRelate} | R Documentation |
Convert a PLINK PED text file to a GDS file.
snpgdsPED2GDS(ped.fn, map.fn, out.gdsfn, family=TRUE, snpfirstdim=FALSE,
compress.annotation="ZIP_RA.max", compress.geno="", verbose=TRUE)
ped.fn |
the file name of PED file, genotype information |
map.fn |
the file name of MAP file |
out.gdsfn |
the output GDS file |
family |
if |
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) |
compress.annotation |
the compression method for the GDS variables,
except "genotype"; optional values are defined in the function
|
compress.geno |
the compression method for "genotype"; optional
values are defined in the function |
verbose |
if TRUE, show information |
GDS – Genomic Data Structures, the extended file name used for storing genetic data, and the file format is used in the gdsfmt package.
PED – PLINK PED format.
None.
Xiuwen Zheng
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
snpgdsGDS2PED, snpgdsBED2GDS,
snpgdsGDS2BED
# open
genofile <- snpgdsOpen(snpgdsExampleFileName())
snpgdsGDS2PED(genofile, "tmp")
# close
snpgdsClose(genofile)
# PED ==> GDS
snpgdsPED2GDS("tmp.ped", "tmp.map", "test.gds")
# delete the temporary file
unlink(c("tmp.ped", "tmp.map", "test.gds"), force=TRUE)