Hi,
Thanks for the report. Now fixed in 1.13.31.
This problem, like the last one you reported, was related to CDSID
becoming an IntegerList. When region=AllVariants, results are combined
and ordered by QUERYID, TXID, CDSID and GENEID. In your example ties
were not broken by QUERYID or TXID and so CDSID was tested. order() does
work on 'List' objects but they must be the only argument. The error was
complaining that when order() has multiple arguments they can't be
'List's. This is a bit of a special case and is why you haven't seen
this error for all runs of locateVariants().
Now that CDSID is an IntegerList (holds multiple values) it doesn't make
sense to include it in the ordering so I have removed it.
Valerie
On 02/16/2015 07:44 AM, Robert Castelo wrote:
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
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109
Email: voben...@fredhutch.org
Phone: (206) 667-3158
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