SNPGDSFileClass-class: SNPGDSFileClass

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Description

A SNPGDSFileClass object provides access to a GDS file containing genome-wide SNP data. It extends the class gds.class in the gdsfmt package.

Author(s)

Xiuwen Zheng

See Also

snpgdsOpen, snpgdsClose

Examples

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

class(genofile)
# "SNPGDSFileClass" "gds.class"

# close the file
snpgdsClose(genofile)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
File: /usr/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 }
[1] "SNPGDSFileClass" "gds.class"      

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.