zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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error in snpgdsPCACorr with SeqArray file #14

Closed smgogarten closed 9 years ago

smgogarten commented 9 years ago

I encountered an error when trying to use the function snpgdsPCACorr with a SeqArray-format GDS file.

library(SeqArray)
library(SNPRelate)
gds.fn <- seqExampleFileName("KG_Phase1")
genofile <- seqOpen(gds.fn)
pca <- snpgdsPCA(genofile)
corr <- snpgdsPCACorr(pca, genofile)

Error in index.gdsn(gdsobj, "snp.id") : Invalid path "snp.id"!

sessionInfo()

R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] SNPRelate_1.3.8 SeqArray_1.9.12 gdsfmt_1.5.12

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.31.17      XVector_0.9.1
 [3] GenomicAlignments_1.5.11   GenomicRanges_1.21.16
 [5] BiocGenerics_0.15.3        zlibbioc_1.15.0
 [7] IRanges_2.3.14             BiocParallel_1.3.34
 [9] BSgenome_1.37.3            GenomeInfoDb_1.5.8
[11] tools_3.2.1                SummarizedExperiment_0.3.2
[13] parallel_3.2.1             Biobase_2.29.1
[15] DBI_0.3.1                  lambda.r_1.1.7
[17] futile.logger_1.4.1        rtracklayer_1.29.12
[19] S4Vectors_0.7.10           futile.options_1.0.0
[21] bitops_1.0-6               RCurl_1.95-4.7
[23] biomaRt_2.25.1             RSQLite_1.0.0
[25] GenomicFeatures_1.21.13    Biostrings_2.37.2
[27] Rsamtools_1.21.13          stats4_3.2.1
[29] XML_3.98-1.3               VariantAnnotation_1.15.20