hi Valerie,
i'm afraid i have hit another cryptic error in locateVariants() related
to some recent update of the devel version of the package, could you
take a look at it? (code below..)
thanks!!
robert.
==========================================
library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
gr <- GRanges("chrX", IRanges(start=128913961, width=1))
loc <- locateVariants(gr, txdb,
AllVariants(intergenic=IntergenicVariants(0, 0)))
Error in ans[order(meta$QUERYID, meta$TXID, meta$CDSID, meta$GENEID), :
error in evaluating the argument 'i' in selecting a method for
function '[': Error in order(c(1L, 1L), c("76534", "76534"),
list(integer(0), integer(0)), :
unimplemented type 'list' in 'listgreater'
4: ans[order(meta$QUERYID, meta$TXID, meta$CDSID, meta$GENEID),
]
3: .local(query, subject, region, ...)
2: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
0)))
1: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
0)))
sessionInfo()
R Under development (unstable) (2014-10-14 r66765)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.18
AnnotationDbi_1.29.17
[4] Biobase_2.27.1 VariantAnnotation_1.13.29
Rsamtools_1.19.27
[7] Biostrings_2.35.8 XVector_0.7.4
GenomicRanges_1.19.37
[10] GenomeInfoDb_1.3.13 IRanges_2.1.38
S4Vectors_0.5.19
[13] BiocGenerics_0.13.4 vimcom_1.0-0
setwidth_1.0-3
[16] colorout_1.0-3
loaded via a namespace (and not attached):
[1] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.9
BiocParallel_1.1.13
[5] biomaRt_2.23.5 bitops_1.0-6 brew_1.0-6
BSgenome_1.35.17
[9] checkmate_1.5.1 codetools_0.2-10 DBI_0.3.1
digest_0.6.8
[13] fail_1.2 foreach_1.4.2
GenomicAlignments_1.3.27 iterators_1.0.7
[17] RCurl_1.95-4.5 RSQLite_1.0.0
rtracklayer_1.27.7 sendmailR_1.2-1
[21] stringr_0.6.2 tools_3.2.0 XML_3.98-1.1
zlibbioc_1.13.1
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