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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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PLINK bed file conversion switch the variant and sample #61

Closed thierrygosselin closed 4 years ago

thierrygosselin commented 4 years ago

I'm trying to import a plink bed file:

test1 <- SeqArray::seqBED2GDS(
    bed.fn = "plink.bed",
    fam.fn = "plink.bim",
    bim.fn = "plink.fam",
    out.gdsfn = "test1.gds",
    compress.geno = "ZIP_RA",
    compress.annotation = "ZIP_RA",
    verbose = TRUE
  ) %>%
    SeqArray::seqOpen(gds.fn = ., readonly = FALSE)

And when I look at the GDS, the number of variant and sample show that their is a switch between the 2. Is it something I'm doing wrong here ?

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thierrygosselin commented 4 years ago

Sorry my mistake, I switched the bim and fam files ...