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Dear List,
I am using your package "GOstats" for my gene expression data. I took
seleceted gene id (entrez id) and gene universrse which is all gens in
the chip we used (entrez id) form excel file provided by the genome
studio software. Here is the code. If you have some available time
I want to you to validate the code .
setwd("W:/KAUSHAL_RESEARCH/K_Surendaran/Data")
source("http://www.bioconductor.org/biocLite.R")
biocLite("AnnotatidatonDbi")
library("AnnotationDbi")
biocLite("illuminaMousev2.db")
library("illuminaMousev2.db")
biocLite("GOstats")
library("GOstats")
biocLite("KEGG.db")
library("KEGG.db")
biocLite("reactome.db")
library("reactome.db")
data1=read.csv("uni_id.csv", header=T) ### gene universe
data2=data.matrix(data1)
colnames(data2)<-NULL
AllID=as.numeric(data2)
head(AllID)
[1] 212772 212772 100039693 56378 74257 20510
data3=read.csv("selec_ID.csv", header=T) ### selected gene
data4=data.matrix(data3)
colnames(data4)<-NULL
SelecID=as.numeric(data4)
head(SelecID)
[1] 74257 20322 59010 66398 50995 242864
getClass("GOHyperGParams")
getClass("KEGGHyperGParams")
params<-new("GOHyperGParams", geneIds=SelecID, universeGeneIds=AllID,
annotation=c("illuminaMousev2"), ontology="BP", pvalueCutoff=0.01,
testDirection="over")
resultBP1<-hyperGTest(params)
resultBP1
summary(resultBP1)
htmlReport(resultBP1, file="ALL_hgo.html")
Partial output:
GOBPID Pvalue OddsRatio ExpCount Count Size Term
GO:0001905 0.000 Inf 0 2 2 activation of
membrane attack complex
I also want to get the genes in the count column.
Thank you very much for help.
-- output of sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] xtable_1.7-1 GO.db_2.9.0
reactome.db_1.44.0
[4] KEGG.db_2.9.1 GOstats_2.26.0 graph_1.38.3
[7] Category_2.26.0 illuminaMousev2.db_1.18.0
org.Mm.eg.db_2.9.0
[10] RSQLite_0.11.4 DBI_0.2-7
AnnotationDbi_1.22.6
[13] Biobase_2.20.1 BiocGenerics_0.6.0
BiocInstaller_1.10.3
loaded via a namespace (and not attached):
[1] annotate_1.38.0 AnnotationForge_1.2.2 genefilter_1.42.0
GSEABase_1.22.0
[5] IRanges_1.18.4 RBGL_1.36.2 splines_3.0.1
stats4_3.0.1
[9] survival_2.37-4 tools_3.0.1 XML_3.98-1.1
--
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