Entering edit mode
Hi,
I am using the topGO package and this is my code:
# input data
head(dat)
ID Entrezid Ensembl logFC AveExpr t P.Value adj.P.Val B fc ctrl
1 17500195 20845 ENSMUSG00000031574 1.350722 8.794343 35.00267 3.322001e-09 2.994419e-05 11.46955 2.550397 8.148782
2 17514553 17394 ENSMUSG00000005800 1.474257 7.718298 34.09233 4.000494e-09 2.994419e-05 11.33943 2.778406 6.971868
3 17435584 231070 ENSMUSG00000045294 1.290198 12.451859 32.98903 5.044790e-09 2.994419e-05 11.17338 2.445615 11.817585
4 17404821 12428 ENSMUSG00000027715 -1.579461 10.139447 -30.63328 8.502606e-09 3.112320e-05 10.78515 -2.988581 10.871834
5 17530311 81907 ENSMUSG00000042757 -1.229960 10.666388 -30.51421 8.739034e-09 3.112320e-05 10.76421 -2.345604 11.303222
6 17358591 77836 ENSMUSG00000024806 2.499764 8.350270 29.64428 1.071285e-08 3.179395e-05 10.60707 5.655928 7.209390
# get geneList
geneList <-as.vector(dat$adj.P.Val)
names(geneList) <- as.character(dat$Ensembl)
# gene selection function
GetGeneList <- function(input){
input < 0.01
}
# GOdata
GOdata <-new ("topGOdata",
ontology = "BP",
allGenes = geneList,
geneSel = GetGeneList,
nodeSize = 10,
annot = annFUN.org,
mapping="org.Mm.eg.db",
ID = "ensembl"
)
# run tests
resultKS <- runTest(GOdata, algorithm = "classic", statistic = "ks")
resultKS.elim <- runTest(GOdata, algorithm = "elim", statistic = "ks")
# run GenTable
allRes <- GenTable(GOdata,
classicKS = resultKS,
orderBy = "elimKS",
topNodes = 25)
# results
head(allRes)
GO.ID Term Annotated Significant Expected classicKS
1 GO:0044699 single-organism process 9632 1200 975.38 < 1e-30
2 GO:0044763 single-organism cellular process 8661 1094 877.06 1.8e-30
3 GO:0008150 biological_process 14717 1523 1490.32 4.1e-26
4 GO:0009987 cellular process 10696 1242 1083.13 6.5e-22
5 GO:0048522 positive regulation of cellular process 3521 443 356.55 7.4e-19
6 GO:0044710 single-organism metabolic process 3547 488 359.19 1.0e-18
# get top 5 GO ids
goid <- as.character(allRes$GO.ID)[1:5]
goid
[1] "GO:0044699" "GO:0044763" "GO:0008150" "GO:0009987" "GO:0048522"
# printGenes function
printGenes(object = GOdata,
whichTerms = goid,
geneCutOff = 500,
chip = 'org.Mm.eg.db')
Error in get(paste(chip, "ENTREZID", sep = "")) :
object 'org.Mm.egENTREZID' not found
# sessionInfo
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10 (Yosemite)
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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] mogene20sttranscriptcluster.db_8.3.1 org.Mm.eg.db_3.1.2 topGO_2.20.0
[4] SparseM_1.6 GO.db_3.1.2 RSQLite_1.0.0
[7] DBI_0.3.1 AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0
[10] IRanges_2.2.4 S4Vectors_0.6.0 Biobase_2.28.0
[13] graph_1.46.0 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] lattice_0.20-31 grid_3.2.0 tools_3.2.0
In the printGenes function, instead of mogene20sttranscriptcluster.db, I want to use org.Mm.eg.db to make the code more generalized but it is throwing an error.
How can I use org.Mm.eg.db or org.Hs.eg.db instead of specific chip in the printGenes function?
