## ----eval=FALSE------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("fCI") ## ---- warning = FALSE, message = FALSE------------------------------------- suppressPackageStartupMessages(library(fCI)) library(fCI) ## -------------------------------------------------------------------------- fci.data=data.frame(matrix(sample(3:100, 1043*6, replace=TRUE), 1043,6)) fci.data=total.library.size.normalization(fci.data) ## -------------------------------------------------------------------------- fci.data=data.frame(matrix(sample(3:100, 1043*6, replace=TRUE), 1043,6)) fci.data=trim.size.normalization(fci.data) ## -------------------------------------------------------------------------- pkg.path=path.package('fCI') filename=paste(pkg.path, "/extdata/Supp_Dataset_part_2.txt", sep="") if(file.exists(filename)){ fci=new("NPCI") fci=find.fci.targets(fci, c(1,2,3), c(4,5,6), filename) } ## -------------------------------------------------------------------------- Diff.Expr.Genes=show.targets(fci) head(Diff.Expr.Genes) ## -------------------------------------------------------------------------- figures(fci) ## -------------------------------------------------------------------------- fci=find.fci.targets(fci, c(1,2), 5, filename) ## -------------------------------------------------------------------------- if(file.exists(filename)){ Diff.Expr.Genes=fCI.call.by.index(c(1,2,3), c(4,5,6), filename) head(Diff.Expr.Genes) } ## ---- results='asis'------------------------------------------------------- fci.data=data.frame(matrix(sample(3:100, 1043*6, replace=TRUE), 1043,6)) ## ---- warning = FALSE, message = FALSE------------------------------------- library(fCI) fci=new("NPCI") targets=find.fci.targets(fci, c(1,2,3), c(4,5,6), fci.data) Diff.Expr.Genes=show.targets(targets) head(Diff.Expr.Genes) figures(targets) ## -------------------------------------------------------------------------- fci=new("NPCI") filename2=paste(pkg.path, "/extdata/proteoGenomics.txt", sep="") if(file.exists(filename2)){ targets=find.fci.targets(fci, list(1:2, 7:8), list(5:6, 11:12), filename2) Diff.Expr.Genes=show.targets(targets) head(Diff.Expr.Genes) } ## -------------------------------------------------------------------------- proteogenomic.data=read.csv(filename2, sep="\t") head(proteogenomic.data) ## -------------------------------------------------------------------------- fci=new("NPCI") fci=setfCI(fci, 7:8, 11:12, seq(from=1.1,to=3,by=0.1), TRUE) ## -------------------------------------------------------------------------- if(file.exists(filename2)){ fci=find.fci.targets(fci, 7:8, 11:12, filename2) head(show.targets(fci)) } figures(fci)