snpgdsOpen: Open a SNP GDS File
In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Description Usage Arguments Details Value Author(s) See Also Examples

Open a SNP GDS file

1	snpgdsOpen(filename, readonly=TRUE, allow.duplicate=FALSE, allow.fork=TRUE)

`filename`	the file name
`readonly`	whether read-only or not
`allow.duplicate`	if `TRUE`, it is allowed to open a GDS file with read-only mode when it has been opened in the same R session, see `openfn.gds`
`allow.fork`	`TRUE` for parallel environment using forking, see `openfn.gds`

It is strongly suggested to call snpgdsOpen instead of openfn.gds, since snpgdsOpen will perform internal checking for data integrality.

Return an object of class SNPGDSFileClass.

Xiuwen Zheng

snpgdsClose

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

genofile

# close the file
snpgdsClose(genofile)

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
File: /usr/local/lib/R/site-library/SNPRelate/extdata/hapmap_geno.gds (709.6K)
+    [  ] *
|--+ sample.id   { VStr8 279 ZIP(29.9%), 679B }
|--+ snp.id   { Int32 9088 ZIP(34.8%), 12.3K }
|--+ snp.rs.id   { VStr8 9088 ZIP(40.1%), 36.2K }
|--+ snp.position   { Int32 9088 ZIP(94.7%), 33.6K }
|--+ snp.chromosome   { UInt8 9088 ZIP(0.94%), 85B } *
|--+ snp.allele   { VStr8 9088 ZIP(11.3%), 4.0K }
|--+ genotype   { Bit2 279x9088, 619.0K } *
\--+ sample.annot   [ data.frame ] *
   |--+ family.id   { VStr8 279 ZIP(34.4%), 514B }
   |--+ father.id   { VStr8 279 ZIP(31.5%), 220B }
   |--+ mother.id   { VStr8 279 ZIP(30.9%), 214B }
   |--+ sex   { VStr8 279 ZIP(17.0%), 95B }
   \--+ pop.group   { VStr8 279 ZIP(6.18%), 69B }