GO_over

GO_over.r

source('source_https.r')
## You can now source R scripts from GitHub. The RAW URL is needed.
source_https('https://raw.github.com/bobthecat/codebox/master/GO_over.r')

## Define the universe
library(mouse4302.db)
uniqueId <- unique(as.vector(unlist(as.list(mouse4302ENTREZID))))
entrezUniverse <- uniqueId[!is.na(uniqueId)]
length(entrezUniverse)
[1] 20877

## ORA with conditional hypergeometric test
mfhyper <- GO_over(entrezUniverse, glist, annot='mouse4302.db')

## Information on the Directed Acyclic Graph (DAG)
goDag(mfhyper)
A graphNEL graph with directed edges
Number of Nodes = 2723 
Number of Edges = 5643 

## How many gene were mapped in the end?
geneMappedCount(mfhyper)
[1] 257

## Write out the results
source_https('https://raw.github.com/bobthecat/codebox/master/write.GOhyper.r')

mrnaGO <- write.GOhyper(mfhyper, filename="BP_mRNA_significant.xls")
dim(mrnaGO <- mrnaGO[mrnaGO$adjPvalue <= 0.05,])
[1] 59  8

head(mrnaGO)
      GOBPID       Pvalue    adjPvalue OddsRatio   ExpCount Count Size                                              Term
1 GO:0007275 7.195117e-09 4.245119e-07  2.238934 47.7311790    86 3138              multicellular organismal development
2 GO:0031116 9.123574e-07 2.691454e-05 41.247520  0.1977391     5   13 positive regulation of microtubule polymerization
3 GO:0007155 6.134458e-06 1.206443e-04  2.792433 11.0429688    28  726                                     cell adhesion
4 GO:0048699 9.122060e-06 1.345504e-04  2.630388 12.5640388    30  826                             generation of neurons
5 GO:0048468 1.143166e-05 1.348936e-04  2.326166 18.1463660    38 1193                                  cell development
6 GO:0031399 2.234055e-05 2.196821e-04  2.586734 11.8491359    28  779        regulation of protein modification process