Hi
I am having problems with reporting tools.To be simple I am including the same example as in Category package and then try to do html with Reporting Tools but I get an error. (R studio sometimes crashes with this) any help is appreciated.
Mayte
library("hgu95av2.db") library("annotate") probids <- ls(hgu95av2GENENAME)[1:300] ## Select for probeids that have PFAM ids hasPFAM <- sapply(mget(probids, hgu95av2PFAM), function(ids) if(!is.na(ids) && length(ids) > 1) TRUE else FALSE) probids <- probids[hasPFAM] ## get unique Entrez Gene IDs probids <- unique(getEG(probids, "hgu95av2")) ## Now do the same for the universe univ <- ls(hgu95av2GENENAME) univHasPFAM <- sapply(mget(univ, hgu95av2PFAM), function(ids) if(!is.na(ids) && length(ids) > 1) TRUE else FALSE) univ <- univ[univHasPFAM] univ <- unique(getEG(univ, "hgu95av2")) p <- new("PFAMHyperGParams", geneIds=probids, universeGeneIds=univ, annotation="hgu95av2") ## this takes a while... if(interactive()){ hypt <- hyperGTest(p) summary(hypt) htmlReport(hypt, file="temp.html", summary.args=list("htmlLinks"=TRUE)) } library(ReportingTools) Report <-HTMLReport(shortName ="PFAM analysis", title='PFAM analysis',reportDirectory='./myoutput',baseUrl = "") ReportingTools::publish(hypt, Report, selectedIDs=probids, annotation.db="org.Hs.eg", categorySize=20,makePlot=FALSE) Error in if (dim(df)[1] < 1) { : argument is of length zero sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ReportingTools_2.4.0 knitr_1.6 xtable_1.7-4 annotate_1.42.1 hgu95av2.db_2.14.0 org.Hs.eg.db_2.14.0 [7] Category_2.30.0 GO.db_2.14.0 RSQLite_0.11.4 DBI_0.3.0 Matrix_1.1-4 AnnotationDbi_1.26.0 [13] GenomeInfoDb_1.0.2 Biobase_2.24.0 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 AnnotationForge_1.6.1 BatchJobs_1.3 BBmisc_1.7 BiocParallel_0.6.1 [6] biomaRt_2.20.0 Biostrings_2.32.1 biovizBase_1.12.3 bitops_1.0-6 brew_1.0-6 [11] BSgenome_1.32.0 checkmate_1.4 cluster_1.15.3 codetools_0.2-9 colorspace_1.2-4 [16] DESeq2_1.4.5 dichromat_2.0-0 digest_0.6.4 edgeR_3.6.8 evaluate_0.5.5 [21] fail_1.2 foreach_1.4.2 foreign_0.8-61 formatR_1.0 Formula_1.1-2 [26] genefilter_1.46.1 geneplotter_1.42.0 GenomicAlignments_1.0.6 GenomicFeatures_1.16.2 GenomicRanges_1.16.4 [31] ggbio_1.12.10 ggplot2_1.0.0 GOstats_2.30.0 graph_1.42.0 grid_3.1.1 [36] gridExtra_0.9.1 GSEABase_1.26.0 gtable_0.1.2 Hmisc_3.14-5 hwriter_1.3.2 [41] IRanges_1.22.10 iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 limma_3.20.9 [46] locfit_1.5-9.1 MASS_7.3-34 munsell_0.4.2 nnet_7.3-8 PFAM.db_2.14.0 [51] plyr_1.8.1 proto_0.3-10 R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.33.0 [56] RBGL_1.40.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RcppArmadillo_0.4.400.0 RCurl_1.95-4.3 [61] reshape2_1.4 rpart_4.1-8 Rsamtools_1.16.1 rtracklayer_1.24.2 scales_0.2.4 [66] sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 stringr_0.6.2 survival_2.37-7 [71] tools_3.1.1 VariantAnnotation_1.10.5 XML_3.98-1.1 XVector_0.4.0 zlibbioc_1.10.0