seqSNP2GDS {SeqArray} | R Documentation |
Converts a SNP GDS file to a SeqArray GDS file.
seqSNP2GDS(gds.fn, out.fn, storage.option="LZMA_RA", major.ref=TRUE, ds.type=c("packedreal16", "float", "double"), optimize=TRUE, digest=TRUE, verbose=TRUE)
gds.fn |
the file name of SNP format |
out.fn |
the file name, output a file of SeqArray format |
storage.option |
specify the storage and compression options,
|
major.ref |
if TRUE, use the major allele as a reference allele; otherwise, use A allele in SNP GDS file as a reference allele |
ds.type |
applicable when import dosages, the data type for storing
dosages; see |
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. If the input
file is genotype dosage, the dosage matrix is stored in the node
annotation/format/DS
with the estimated dosage of alternative alleles.
Any value less than 0 or greater than 2 will be replaced by NaN.
Xiuwen Zheng
seqGDS2SNP
, seqVCF2GDS
,
seqGDS2VCF
, seqBED2GDS
library(SNPRelate) # the GDS file gds.fn <- snpgdsExampleFileName() seqSNP2GDS(gds.fn, "tmp.gds") seqSummary("tmp.gds") # remove the temporary file unlink("tmp.gds", force=TRUE)