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[Bioc-devel] AnnotationDbi and select function
6 messages · Servant Nicolas, James W. MacDonald, Marc Carlson
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'?valuation de l'argument 'x' lors de la s?lection d'une m?thode 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 [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
Thanks Nicolaus! That's a good bug. I will work on a fix. The reason why James work-around here functions is because the number of databases that it has to query is fewer by one. It is also faster for this reason. So when you say GENEID you mean the ids used in the associated txdb database which means that these have to be checked against that DB (and anything related to it extracted) and then merged with the results of the symbol information by joining on the foreign key for these two DBs. So thats actually much more complex than just extracting all the same data from just the org package even though the end result (in this case) is the same. The bug is probably happening in the associated merge step. Marc
On 03/12/2014 10:06 AM, James W. MacDonald wrote:
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'?valuation de l'argument 'x' lors de la s?lection d'une
m?thode 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
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi guys, Thanks for your feedbacks. Indeed I put GENEID because it is used in the txdb database.
library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene columns(txdb)
[1] "CDSID" "CDSNAME" "CDSCHROM" "CDSSTRAND" "CDSSTART" [6] "CDSEND" "EXONID" "EXONNAME" "EXONCHROM" "EXONSTRAND" [11] "EXONSTART" "EXONEND" "GENEID" "TXID" "EXONRANK" [16] "TXNAME" "TXCHROM" "TXSTRAND" "TXSTART" "TXEND" I will move to ENTREZID which is much faster ! I'm glad It could help Nicolas ________________________________________ De : bioc-devel-bounces at r-project.org [bioc-devel-bounces at r-project.org] de la part de Marc Carlson [mcarlson at fhcrc.org] Date d'envoi : mercredi 12 mars 2014 20:18 ? : bioc-devel at r-project.org Objet : Re: [Bioc-devel] AnnotationDbi and select function Thanks Nicolaus! That's a good bug. I will work on a fix. The reason why James work-around here functions is because the number of databases that it has to query is fewer by one. It is also faster for this reason. So when you say GENEID you mean the ids used in the associated txdb database which means that these have to be checked against that DB (and anything related to it extracted) and then merged with the results of the symbol information by joining on the foreign key for these two DBs. So thats actually much more complex than just extracting all the same data from just the org package even though the end result (in this case) is the same. The bug is probably happening in the associated merge step. Marc
On 03/12/2014 10:06 AM, James W. MacDonald wrote:
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'?valuation de l'argument 'x' lors de la s?lection d'une
m?thode 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
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
I just checked a fix in for this bug to GenomicFeatures (which happens to be where the problem was). It should percolate out to the build system soon. Marc
On 03/12/2014 02:19 PM, Servant Nicolas wrote:
Hi guys, Thanks for your feedbacks. Indeed I put GENEID because it is used in the txdb database.
library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene columns(txdb)
[1] "CDSID" "CDSNAME" "CDSCHROM" "CDSSTRAND" "CDSSTART" [6] "CDSEND" "EXONID" "EXONNAME" "EXONCHROM" "EXONSTRAND" [11] "EXONSTART" "EXONEND" "GENEID" "TXID" "EXONRANK" [16] "TXNAME" "TXCHROM" "TXSTRAND" "TXSTART" "TXEND" I will move to ENTREZID which is much faster ! I'm glad It could help Nicolas
________________________________________
De : bioc-devel-bounces at r-project.org [bioc-devel-bounces at r-project.org] de la part de Marc Carlson [mcarlson at fhcrc.org]
Date d'envoi : mercredi 12 mars 2014 20:18
? : bioc-devel at r-project.org
Objet : Re: [Bioc-devel] AnnotationDbi and select function
Thanks Nicolaus! That's a good bug. I will work on a fix. The reason
why James work-around here functions is because the number of databases
that it has to query is fewer by one. It is also faster for this
reason. So when you say GENEID you mean the ids used in the associated
txdb database which means that these have to be checked against that DB
(and anything related to it extracted) and then merged with the results
of the symbol information by joining on the foreign key for these two
DBs. So thats actually much more complex than just extracting all the
same data from just the org package even though the end result (in this
case) is the same. The bug is probably happening in the associated
merge step.
Marc
On 03/12/2014 10:06 AM, James W. MacDonald wrote:
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'?valuation de l'argument 'x' lors de la s?lection d'une
m?thode 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
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
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Also, There is nothing wrong with using GENEID the way that you initially did. It was just a small bug that prevented some internal subsetting from working properly and that is now fixed. It just happened that GENEID was equivalent to ENTREZID in this case. And that ends up making it a slower choice just because the software has to do more work (in case GENEID is something else). So since you know that these are in fact ENTREZIDs, you can take Jims suggestion as a short cut and thus get a little performance boost. But it's still a less specific thing to request than GENEID (which could potentially be another kind of ID). So the two things (GENEID and ENTREZID) are not always the same kind of thing. They just happened to both be ENTREZID in *this* case. In a different scenario GENEID from the associated TranscriptDb might be something like an ensembl gene ID. And then to use a shortcut would mean using ENSEMBL instead of ENTREZID to do the shortcut... In contrast: GENEID should normally always work (but it should also be a tiny bit slower). Sorry if you know all this stuff, but I think its better to be explicit than to say too little. Marc
On 03/12/2014 02:53 PM, Marc Carlson wrote:
I just checked a fix in for this bug to GenomicFeatures (which happens to be where the problem was). It should percolate out to the build system soon. Marc On 03/12/2014 02:19 PM, Servant Nicolas wrote:
Hi guys, Thanks for your feedbacks. Indeed I put GENEID because it is used in the txdb database.
library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene columns(txdb)
[1] "CDSID" "CDSNAME" "CDSCHROM" "CDSSTRAND" "CDSSTART" [6] "CDSEND" "EXONID" "EXONNAME" "EXONCHROM" "EXONSTRAND" [11] "EXONSTART" "EXONEND" "GENEID" "TXID" "EXONRANK" [16] "TXNAME" "TXCHROM" "TXSTRAND" "TXSTART" "TXEND" I will move to ENTREZID which is much faster ! I'm glad It could help Nicolas
________________________________________
De : bioc-devel-bounces at r-project.org
[bioc-devel-bounces at r-project.org] de la part de Marc Carlson
[mcarlson at fhcrc.org]
Date d'envoi : mercredi 12 mars 2014 20:18
? : bioc-devel at r-project.org
Objet : Re: [Bioc-devel] AnnotationDbi and select function
Thanks Nicolaus! That's a good bug. I will work on a fix. The reason
why James work-around here functions is because the number of databases
that it has to query is fewer by one. It is also faster for this
reason. So when you say GENEID you mean the ids used in the associated
txdb database which means that these have to be checked against that DB
(and anything related to it extracted) and then merged with the results
of the symbol information by joining on the foreign key for these two
DBs. So thats actually much more complex than just extracting all the
same data from just the org package even though the end result (in this
case) is the same. The bug is probably happening in the associated
merge step.
Marc
On 03/12/2014 10:06 AM, James W. MacDonald wrote:
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'?valuation de l'argument 'x' lors de la s?lection d'une
m?thode 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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