[Bioc-devel] Broken pathway in graphite package?
Ryan C. Thompson
rct at thompsonclan.org
Tue Jun 16 22:25:56 CEST 2015
Thanks Ivana,
I've forwarded your message to the bioc-devel list so graphite
developers can see it.
-Ryan
On 06/16/2015 12:46 PM, ihnatova at iba.muni.cz wrote:
> Hello,
>
> this problem is caused by the presence of interaction type
> "control(In(INHIBITION-COMPETITIVE))" which is missing in the
> unexported spiaConv table and that leads to NA's during the
> processing. It must be fixed by package maintainer. You will run into
> same problems with these pathways:
>
> Insulin receptor signalling cascade IRS
> activation IRS-related events
> SHC activation
> 651 691
> 693 1197
> SHC-related events Signaling by Insulin
> receptor Signaling Pathways
> 1203 1235
> 1263
>
>
> Ivana
>
>
> Dne 2015-06-16 21:17, Ryan C. Thompson napsal:
>> Hello,
>>
>> I was attempting to run SPIA through the graphite package and ran into
>> an odd error when running prepareSPIA on the human Reactome pathways.
>> You can reproduce the error simply and quickly by:
>>
>>> library(graphite)
>>> prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor
>>> signalling cascade"], "test", TRUE)
>> Insulin receptor signalling cascade
>> Error in Filter(Negate(is.null), lapply(db, function(p) { :
>> error in evaluating the argument 'x' in selecting a method for
>> function 'Filter': Error in if (e[1] <= e[2]) paste(e[1], e[2], sep =
>> "|") else paste(e[2], :
>> missing value where TRUE/FALSE needed
>>
>> The traceback is not particularly informative. I don't actually see
>> the line of code from the error message in the traceback:
>>
>>> traceback()
>> 4: Filter(Negate(is.null), lapply(db, function(p) {
>> if (print.names)
>> cat(p at title, "\n")
>> p <- convertIdentifiers(p, "entrez")
>> es <- edges(p)
>> if (NROW(es) == 0 || NROW(unique(es[, 1:2])) < 5)
>> return(NULL)
>> ns <- nodes(p)
>> es <- merge(es, spiaConv, all.x = TRUE)[c("src", "dest",
>> "direction", "spiaType")]
>> l <- sapply(spiaAttributes, simplify = FALSE, USE.NAMES = TRUE,
>> function(edgeType) {
>> est <- es[es[, 4] == edgeType, , drop = FALSE]
>> gnl <- buildGraphNEL(ns, est, TRUE)
>> t(as(gnl, "matrix"))
>> })
>> l$title <- p at title
>> l$nodes <- ns
>> l$NumberOfReactions <- 0
>> return(l)
>> }))
>> 3: .prepareSPIA(db at entries, pathwaySetName, print.names)
>> 2: prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor
>> signalling cascade"],
>> "test", TRUE)
>> 1: prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor
>> signalling cascade"],
>> "test", TRUE)
>>
>> I guess for now I will remove the offending pathway, but it seems
>> unexpected that graphite cannot handle a pathway included in its own
>> package.
>>
>> -Ryan Thompson
>>
>>> sessionInfo()
>> R version 3.2.0 (2015-04-16)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> Running under: Ubuntu 14.04.2 LTS
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] grDevices datasets parallel graphics stats4 stats utils
>> [8] methods base
>>
>> other attached packages:
>> [1] org.Hs.eg.db_3.1.2 GSEABase_1.30.2
>> [3] graph_1.46.0 annotate_1.46.0
>> [5] XML_3.98-1.2 graphite_1.14.0
>> [7] openxlsx_2.5.10 DESeq2_1.8.1
>> [9] RcppArmadillo_0.5.200.1.0 Rcpp_0.11.6
>> [11] edgeR_3.10.2 limma_3.24.10
>> [13] magrittr_1.5 dplyr_0.4.1
>> [15] biomaRt_2.24.0 functional_0.6
>> [17] sqldf_0.4-10 RSQLite_1.0.0
>> [19] DBI_0.3.1 gsubfn_0.6-6
>> [21] proto_0.3-10 GenomicFeatures_1.20.1
>> [23] AnnotationDbi_1.30.1 chipseq_1.18.0
>> [25] BSgenome_1.36.0 inline_0.3.14
>> [27] affy_1.46.1 rtracklayer_1.28.4
>> [29] Biobase_2.28.0 ShortRead_1.26.0
>> [31] GenomicAlignments_1.4.1 BiocParallel_1.3.16
>> [33] Rsamtools_1.20.4 Biostrings_2.36.1
>> [35] XVector_0.8.0 GenomicRanges_1.20.5
>> [37] GenomeInfoDb_1.4.0 doParallel_1.0.8
>> [39] iterators_1.0.7 foreach_1.4.2
>> [41] plyr_1.8.3 stringr_1.0.0
>> [43] IRanges_2.2.4 ggplot2_1.0.1
>> [45] S4Vectors_0.6.0 BiocGenerics_0.14.0
>> [47] BiocInstaller_1.18.3
>>
>> loaded via a namespace (and not attached):
>> [1] splines_3.2.0 assertthat_0.1 Formula_1.2-1
>> [4] latticeExtra_0.6-26 lattice_0.20-31 chron_2.3-45
>> [7] digest_0.6.8 RColorBrewer_1.1-2 colorspace_1.2-6
>> [10] preprocessCore_1.30.0 genefilter_1.50.0 zlibbioc_1.14.0
>> [13] xtable_1.7-4 scales_0.2.5 affyio_1.36.0
>> [16] lazyeval_0.1.10 nnet_7.3-9 survival_2.38-2
>> [19] MASS_7.3-40 hwriter_1.3.2 foreign_0.8-63
>> [22] tools_3.2.0 munsell_0.4.2 locfit_1.5-9.1
>> [25] cluster_2.0.1 lambda.r_1.1.7 compiler_3.2.0
>> [28] futile.logger_1.4.1 grid_3.2.0 RCurl_1.96-0
>> [31] bitops_1.0-6 gtable_0.1.2 codetools_0.2-11
>> [34] reshape2_1.4.1 gridExtra_0.9.1 Hmisc_3.16-0
>> [37] futile.options_1.0.0 stringi_0.4-1 geneplotter_1.46.0
>> [40] rpart_4.1-9 acepack_1.3-3.3
>>>
>>
>> _______________________________________________
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