seqSNP2GDS: Convert SNPRelate Format to SeqArray Format

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Convert SNPRelate Format to SeqArray Format

Description

Converts a SNP GDS file to a SeqArray GDS file.

Usage

seqSNP2GDS(gds.fn, out.fn, storage.option="LZMA_RA", major.ref=TRUE,
    ds.type=c("packedreal16", "float", "double"), optimize=TRUE, digest=TRUE,
    verbose=TRUE)

Arguments

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, "LZMA_RA" to use LZMA compression algorithm with higher compression ratio compared to "ZIP_RA"
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 add.gdsn; ds.type="packedreal16" by default
optimize	if TRUE, optimize the access efficiency by calling cleanup.gds
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 TRUE, show information

Value

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.

Author(s)

Xiuwen Zheng

See Also

seqGDS2SNP, seqVCF2GDS, seqGDS2VCF, seqBED2GDS

Examples

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)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.