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zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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error: #67

Closed yangli-ai closed 2 years ago

yangli-ai commented 3 years ago

I used seqSNP2GDS function to convert SNP GDS file into SeqArray GDS file. When I try to do seqGetData(seqvargds, "genotype"), it gives error: Invalid dimension of 'genotype/data' .

seqGetData(seqvar, "allele")[1:20] gives results like: [1] "G,A" "C,T" "T,TC" "C,A" "A,G" "G,GA" "T,G" "A,G" "C,A" "C,T" [11] "C,T" "C,CT" "A,C" "T,A" "C,A" "C,T" "C,T" "T,C" "T,C" "C,T"

How can I find where the problem is? My original SNP GDS file? This file doesn't have problem, as I used it in association test with GENESIS package. Everything is ok there.

zhengxwen commented 3 years ago

If your SNP GDS file stores imputed dosages, please use seqGetData(server, "annotation/format/DS") to access the data.

yangli-ai commented 3 years ago

Thanks.