Question: How to get genes corresponding to a GO term from topGOData object?
gravatar for rishi.dasroy
2.5 years ago by
rishi.dasroy10 wrote:


I have a topGOdata object which is built with following command

> GOdata <- new("topGOdata",
                     description = "Simple session", ontology = "BP",
                     allGenes = na.omit(t), geneSel = topDiffGenes,
                     nodeSize = 10, annot = annFUN.gene2GO, gene2GO = microGeneID2GO)

> resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
> resultKS <- runTest(GOdata, algorithm = "classic", statistic = "ks")
> resultKS.elim <- runTest(GOdata, algorithm = "elim", statistic = "ks")
> allRes_topDiffGenes_.05 <- GenTable(GOdata, classicFisher = resultFisher,
                   classicKS = resultKS, elimKS = resultKS.elim,
                   orderBy = "elimKS",  ranksOf = "classicFisher", topNodes = 11)

With the help of following termStat ,

> termStat(GOdata,"GO:0051797")
           Annotated Significant Expected
GO:0051797        11          10     1.98

Now how can I extract the list of annotated and significant genes correspond to GO:0051797? I am getting following errors

> printGenes(GOdata,whichTerms = "GO:0051797")
Error in sub(".db$", "", chip) :
argument "chip" is missing, with no default

Please help,


> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

 [1] LC_CTYPE=fi_FI.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB          
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB          LC_PAPER=en_GB.UTF-8       LC_NAME=C                 

attached base packages:
 [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GOplot_1.0.1         genefilter_1.52.1   plyr_1.8.3           RColorBrewer_1.1-2   gridExtra_2.2.1     
 [7] ggdendro_0.1-18      ggplot2_2.1.0        ROCR_1.0-7           gplots_2.17.0        topGO_2.22.0         SparseM_1.7         
[13] GO.db_3.2.2          RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.32.3 IRanges_2.4.8        S4Vectors_0.8.11    
[19] Biobase_2.30.0       graph_1.48.0         BiocGenerics_0.16.1  mGSZm_1.0            limma_3.26.8         GenomeGraphs_1.30.0
[25] biomaRt_2.26.1      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3            lattice_0.20-33        listenv_0.6.0          gtools_3.5.0           digest_0.6.9          
 [6] aroma.core_3.0.0       R.devices_2.14.0       R.huge_0.9.0           BiocInstaller_1.20.1   zlibbioc_1.16.0       
[11] annotate_1.48.0        gdata_2.17.0           R.utils_2.2.0          R.oo_1.20.0            preprocessCore_1.32.0
[16] labeling_0.3           splines_3.2.2          RCurl_1.95-4.8         munsell_0.4.3          base64enc_0.1-3       
[21] aroma.apd_0.6.0        R.rsp_0.21.0           globals_0.6.1          DNAcopy_1.44.0         codetools_0.2-14      
[26] matrixStats_0.50.1     XML_3.98-1.4           future_0.12.0          MASS_7.3-45            bitops_1.0-6          
[31] R.methodsS3_1.7.1      xtable_1.8-2           gtable_0.2.0           affy_1.48.0            scales_0.4.0          
[36] KernSmooth_2.23-15     aroma.affymetrix_3.0.0 PSCBS_0.61.0           affyio_1.40.0          R.filesets_2.10.0     
[41] tools_3.2.2            Cairo_1.5-9            R.cache_0.12.0         survival_2.38-3        colorspace_1.2-6      
[46] caTools_1.17.1      


ADD COMMENTlink modified 14 months ago by mt10220 • written 2.5 years ago by rishi.dasroy10
gravatar for mt1022
14 months ago by
mt10220 wrote:

By looking through its source code, I find a workaround:

go.ids <-  "GO:0051797"
# extract annotated genes in each term -> a list
term.genes <- genesInTerm(, go.ids)
# extract scores for genes in each term
term.gene.scores <- lapply(term.genes, function(x) stack(geneScore(, x)))




ADD COMMENTlink modified 14 months ago • written 14 months ago by mt10220
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 301 users visited in the last hour