completeFunctionalRegulationAnalysis {CoFRA}

This function performs complete functional regulation analysis

Description

This function performs complete functional regulation analysis

Usage

completeFunctionalRegulationAnalysis(dfPro, func, Fac, dfComp,
  NbackGround = length(unique(unlist(func))), DataExtract = "FDR",
  minCounts = 10, Test = "t.test", no_cores = -1)

Arguments

dfPro

data frame with quantitative values

func

data frame defining which gene ontology to use "BP","CC","MF"

Fac

factor describing the sample groups

dfComp

df containing the comparisons to perform

NbackGround

integer number of total proteins

DataExtract

string which P value correction to use

minCounts

integer minimum number of matching genes for functional category

Test

"t.test" or "wilcox.test"

no_cores

=-1 (no parelle execution) =0 (number of availble cores -1) >0 (use number of cores)

Examples

library(CoFRA)
data(iBAQ)
Fac=factor(c("MCCTT","MCCTT","MCCTT","MCCT","MCCT","MCCT","MC","MC","MC","MCT","MCT","MCT",
"MTT","MTT","MTT","MT","MT","MT","sN","sN","sN","sNT","sNT","sNT","iN","iN","iN","iNT","iNT","iNT"))
dfComp=data.frame(Con=c("MCCT","MT","MC","iN","sN","AllC,MCCT,MT,MC,iN,sN"),Tre=c("MCCTT","MTT",
"MCT","iNT","sNT","AllT,MCCTT,MTT,MCT,iNT,sNT"))
Func=CoFRA::getFunctionalCategories("CC")
head(str(Func))
CC1=CoFRA::completeFunctionalRegulationAnalysis(iBAQ,Func[100:200],Fac,dfComp,NbackGround=142140)