Hi Nicolas,
On 3/12/2014 12:39 PM, Servant Nicolas wrote:
Dear all,
I have an error using the select function from the AnnotationDbi package.
I try to convert some geneID into Symbol, but for some strange reasons it
crashed.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
isActiveSeq(txdb)[seqlevels(txdb)] <- FALSE
isActiveSeq(txdb)[c("chr16","chr1")] <- TRUE
geneGR <- exonsBy(txdb, "gene")
library(Homo.sapiens)
symbol <- select(Homo.sapiens, keys = names(geneGR), keytype = "GENEID", columns =
"SYMBOL")
Erreur dans head(select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype =
"GENEID", :
erreur d'évaluation de l'argument 'x' lors de la sélection d'une méthode
pour la fonction 'head' : Erreur dans res[, .reverseColAbbreviations(x,
cnames), drop = FALSE] :
length(geneGR)
[1] 3269
## The first 1K work
symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1000], keytype = "GENEID", columns
= "SYMBOL")
## The 1K+1 does not !
symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype = "GENEID", columns
= "SYMBOL")
Erreur dans res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
nombre de dimensions incorrect
It looks like I cannot convert more than 1K elements ?? Any reason for that ?
Thank you very much
Nicolas
Not sure what 'GENEID' is in this context - it appears to be Entrez
Gene. But anyway, if you use "ENTREZID" instead, it works fine:
> symbol <- select(Homo.sapiens, names(geneGR), "SYMBOL", "ENTREZID")
> symbol <- select(Homo.sapiens, names(geneGR), "GENEID", "ENTREZID")
Error in res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
incorrect number of dimensions
> symbol <- select(Homo.sapiens, names(geneGR)[1:1000], "GENEID",
"ENTREZID")
> symbol <- select(Homo.sapiens, names(geneGR)[1:1001], "GENEID",
"ENTREZID")
Error in res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
incorrect number of dimensions
Best,
Jim
sessionInfo()
R Under development (unstable) (2014-03-05 r65125)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Homo.sapiens_1.1.2
[2] org.Hs.eg.db_2.10.1
[3] GO.db_2.10.1
[4] RSQLite_0.11.4
[5] DBI_0.2-7
[6] OrganismDbi_1.5.3
[7] XVector_0.3.7
[8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
[9] GenomicFeatures_1.15.9
[10] AnnotationDbi_1.25.14
[11] GenomeInfoDb_0.99.17
[12] Biobase_2.23.6
[13] GenomicRanges_1.15.32
[14] IRanges_1.21.32
[15] BiocGenerics_0.9.3
[16] RColorBrewer_1.0-5
[17] reshape2_1.2.2
[18] reshape_0.8.4
[19] plyr_1.8.1
[20] ggplot2_0.9.3.1
[21] Matrix_1.1-2-2
loaded via a namespace (and not attached):
[1] BatchJobs_1.2 BBmisc_1.5
[3] BiocParallel_0.5.16 biomaRt_2.19.3
[5] Biostrings_2.31.14 bitops_1.0-6
[7] brew_1.0-6 BSgenome_1.31.12
[9] codetools_0.2-8 colorspace_1.2-4
[11] dichromat_2.0-0 digest_0.6.4
[13] fail_1.2 foreach_1.4.1
[15] GenomicAlignments_0.99.29 graph_1.41.3
[17] grid_3.1.0 gtable_0.1.2
[19] iterators_1.0.6 labeling_0.2
[21] lattice_0.20-27 MASS_7.3-29
[23] munsell_0.4.2 proto_0.3-10
[25] RBGL_1.39.2 Rcpp_0.11.0
[27] RCurl_1.95-4.1 Rsamtools_1.15.32
[29] rtracklayer_1.23.15 scales_0.2.3
[31] sendmailR_1.1-2 stats4_3.1.0
[33] stringr_0.6.2 tools_3.1.0
[35] XML_3.98-1.1 zlibbioc_1.9.0
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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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