zhengxwen / gds2bgen

R package for the format conversion from bgen to gds
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genotype conversion doesn't work #4

Closed CreRecombinase closed 3 years ago

CreRecombinase commented 3 years ago

It appears that while it is possible to obtain dosage information from bgen files using dosage=TRUE, using geno=TRUE doesn't work:

> bgen_fn <- system.file("extdata", "example.8bits.bgen", package="gds2bgen")
> seqBGEN2GDS(bgen_fn,"example.gds",geno=TRUE,dosage=FALSE,prob=FALSE,parallel=4)
...
> si <- seqOpen("example.gds")
> si
Object of class "SeqVarGDSClass"
File: /scratch/t.cri.nknoblauch/intersect_snplist/example.gds (6.8K)
+    [  ] *
|--+ description   [  ] *
|--+ sample.id   { Str8 500 LZMA_ra(7.02%), 393B } *
|--+ variant.id   { Int32 199 LZMA_ra(33.9%), 277B } *
|--+ position   { Int32 199 LZMA_ra(60.6%), 489B } *
|--+ chromosome   { Str8 199 LZMA_ra(15.7%), 101B } *
|--+ allele   { Str8 199 LZMA_ra(11.8%), 101B } *
|--+ genotype   [  ] *
|  |--+ data   { Bit2 2x500x0 LZMA_ra, 18B } *
|  |--+ extra.index   { Int32 3x0 LZMA_ra, 18B } *
|  \--+ extra   { Int16 0 LZMA_ra, 18B }
|--+ phase   [  ]
|  |--+ data   { Bit1 500x0 LZMA_ra, 18B } *
|  |--+ extra.index   { Int32 3x0 LZMA_ra, 18B } *
|  \--+ extra   { Bit1 0 LZMA_ra, 18B }
|--+ annotation   [  ]

Any thoughts as to what's happening here? Am i correct that without genotype information, I will be unable to export to plink/BED format?