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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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commit 636df92 breaks creation of SeqVarData objects #49

Closed smgogarten closed 5 years ago

smgogarten commented 5 years ago

After this commit: https://github.com/zhengxwen/SeqArray/commit/636df92126b35f6bb5827b3b0387d06322534251

I get the following error in SeqVarTools:

library(SeqVarTools)
library(Biobase)
gds <- seqOpen(seqExampleFileName("gds"))
sample.id <- seqGetData(gds, "sample.id")
sample.data <- AnnotatedDataFrame(data.frame(sample.id, stringsAsFactors=FALSE))
seqData <- SeqVarData(gds, sample.data)
Error in seqGetData(object, "sample.id") :
  'gdsfile' should be a 'SeqVarGDSClass' object.