### R code from vignette source 'phosphonormalizer.Rnw' ################################################### ### code chunk number 1: phosphonormalizer.Rnw:64-70 (eval = FALSE) ################################################### ## ## ## ## try http:// if https:// URLs are not supported ## if (!requireNamespace("BiocManager", quietly=TRUE)) ## install.packages("BiocManager") ## BiocManager::install("phosphonormalizer") ################################################### ### code chunk number 2: phosphonormalizer.Rnw:75-94 ################################################### #Load the library library(phosphonormalizer) #Specify the column numbers of abundances in the original #data.frame, from both enriched and non-enriched runs samplesCols <- data.frame(enriched=3:17, non.enriched=3:17) #Specify the column numbers of sequence and modification , #in the original data.frame from both enriched and non-enriched runs modseqCols <- data.frame(enriched = 1:2, non.enriched = 1:2) #The samples and their technical replicates techRep <- factor(x = c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5)) #If the parameter plot.fc is set, then the corresponding plots of sample fold changes are produced. #Here, for demonstration, the fold change distributions are shown for samples 3 vs 1 plot.param <- list(control = c(1), samples = c(3)) # Call the function to perform the pairwise normalization: norm <- normalizePhospho(enriched = enriched.rd, non.enriched = non.enriched.rd, samplesCols = samplesCols, modseqCols = modseqCols, techRep = techRep, plot.fc = plot.param)