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