seqBED2GDS {SeqArray} | R Documentation |
Converts a PLINK BED file to a SeqArray GDS file.
seqBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, compress.geno="LZMA_RA", compress.annotation="LZMA_RA", optimize=TRUE, digest=TRUE, verbose=TRUE)
bed.fn |
the file name of binary file, genotype information |
fam.fn |
the file name of first six columns of |
bim.fn |
the file name of extended MAP file: two extra columns = allele names |
out.gdsfn |
the file name, output a file of SeqArray format |
compress.geno |
the compression method for "genotype"; optional
values are defined in the function |
compress.annotation |
the compression method for the GDS variables,
except "genotype"; optional values are defined in the function
|
optimize |
if |
digest |
a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); add hash codes to the GDS file if TRUE or a digest algorithm is specified |
verbose |
if |
Return the file name of SeqArray file with an absolute path.
Xiuwen Zheng
library(SNPRelate) # PLINK BED files bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") fam.fn <- system.file("extdata", "plinkhapmap.fam.gz", package="SNPRelate") bim.fn <- system.file("extdata", "plinkhapmap.bim.gz", package="SNPRelate") # convert seqBED2GDS(bed.fn, fam.fn, bim.fn, "tmp.gds") seqSummary("tmp.gds") # remove the temporary file unlink("tmp.gds", force=TRUE)