## ----setup, include=FALSE------------------------------------------------ knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE---------------------------------------------------------- # ## try http:// if https:// URLs are not supported # source("https://bioconductor.org/biocLite.R") # biocLite("phosphonormalizer") ## ----eval=FALSE---------------------------------------------------------- # #Load the library # library(phosphonormalizer) # #Specifying 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) # #Specifying 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)) # #Call the function # norm <- normalizePhospho(enriched = enriched.rd, non.enriched = non.enriched.rd, # samplesCols = samplesCols, modseqCols = modseqCols, techRep = techRep)