Usage
snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, family=FALSE, snpfirstdim=NA, compress.annotation="ZIP_RA.max", compress.geno="", option=NULL, cvt.chr=c("int", "char"), cvt.snpid=c("auto", "int"), verbose=TRUE)
Arguments
bed.fn
the file name of binary file, genotype information
fam.fn
the file name of first six columns of ".ped"
bim.fn
the file name of extended MAP file:
two extra columns = allele names
out.gdsfn
the output GDS file
family
if TRUE
, to include family information in the
sample annotation
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); NA
, the dimension is
determined by the BED file
compress.annotation
the compression method for the GDS variables,
except "genotype"; optional values are defined in the function
add.gdsn
compress.geno
the compression method for "genotype"; optional
values are defined in the function add.gdsn
cvt.chr
"int"
-- chromosome code in the GDS file is integer;
"char"
-- chromosome code in the GDS file is character
cvt.snpid
"int"
-- to create an integer snp.id
starting from 1; "auto"
-- if SNP IDs in the PLINK file are not
unique, to create an an integer snp.id
, otherwise to use SNP
IDs for snp.id
verbose
if TRUE, show information