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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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Is seqAlleleCount exported? #9

Closed DavisBrian closed 8 years ago

DavisBrian commented 8 years ago

I'm trying to determine if I have an installation error or if a couple functions (seqAlleleCount and seqNumAllele) aren't exported.

library(SeqArray") out_file <- "AA_ARIC_plus_JHS_v2f_chr6.gds" gt_gds = seqOpen(out_file) seqSummary(gt_gds) File: AA_ARIC_plus_JHS_v2f_chr6.gds Sequence Variant Format: v1.0 The number of samples: 3856 The number of variants: 15467 The chromosomes: 6 15467 0 The number of alleles per site: 2 15467 Annotation, information variables: NS, 1, Integer, Number of samples with data AC, A, Float, Allele Count Annotation, format variables: seqAlleleCount(gt_gds) Error: could not find function "seqAlleleCount" seqNumAllele(gt_gds) Error: could not find function "seqNumAllele"

zhengxwen commented 8 years ago

Please run sessionInfo(), show me the version of SeqArray you are using. Please install the latest version, seqAlleleCount() and seqNumAllele() are available in Version>=1.9.6.

DavisBrian commented 8 years ago

Somehow when I pulled from BioConductor this morning it installed 1.8.0. After upgrading it worked.

Thanks!