error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
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Entering edit mode
alyssahz • 0
@aa933c99
Last seen 10 months ago

Hello!

I am trying to apply snpgdsLDpruning to data from the UK Biobank but am running into an error saying, "The GDS node "genotype/data" does not exist." I have converted the downloaded bgen files to gds and tried the code below.

Code:


library(SeqArray)
library(SAIGEgds)
library(SNPRelate)

# gds_fn is the path to our chromosome 22 gds file.
gds <- seqOpen(gds_fn)

set.seed(1000)
snpset <- snpgdsLDpruning(gds)

Output:

Loading required package: gdsfmt
Loading required package: Rcpp
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
SNV pruning based on LD:
Calculating allele counts/frequencies ...
Error in seqApply(f, "genotype", margin = "by.variant", as.is = "list",  :
  The GDS node "genotype/data" does not exist.
Calls: snpgdsLDpruning ... eval -> <Anonymous> -> seqParallel -> FUN -> seqApply
Execution halted

I am new to the GDS file type, so any help and insight would be greatly appreciated. Thanks!

Alyssa

SNPRelate • 247 views
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Entering edit mode

If you used the "gds2bgen" package to convert bgen files to gds, you would need "geno=TRUE" in seqBGEN2GDS(). SNPRelate does not work on dosages, and it needs genotypes.

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