library(dplyr)
context("Normalization functions")
#library(dplyr)
#library(tidyr)
#library(glycanr)
#data(mpiu)
#
#source("../../..//normalizationFunctions_23062015.r")
#
#mw <- mpiu %>%
# spread(glycan, value)
#
##
## tanorm
##
#tmp1 <- totalAreaNorm(mw) %>%
# select(-normalization)
#
#tmp2 <- tanorm(mpiu) %>%
# spread(glycan, value)
#tmp2 <- data.frame(tmp2)
#
#print(all.equal(tmp1, tmp2))
#if(all.equal(tmp1, tmp2)){
# mpiunorm <- tmp2 %>%
# mutate(norm="tanorm")
#}
#
#
#
##
## refPeakNorm
##
#tmp1 <- refPeakNorm(mw) %>%
# select(-normalization)
#
#tmp2 <- refpeaknorm(mpiu) %>%
# spread(glycan, value)
#tmp2 <- data.frame(tmp2)
#
#print(all.equal(tmp1, tmp2))
#if(all.equal(tmp1, tmp2)){
# mpiunorm <- bind_rows(mpiunorm,
# tmp2 %>% mutate(norm="refpeaknorm"))
#}
#
#
##
## mediannorm
##
#tmp1 <- medianNorm(mw) %>%
# select(-normalization)
#
#tmp2 <- mediannorm(mpiu) %>%
# spread(glycan, value)
#tmp2 <- data.frame(tmp2)
#
#print(all.equal(tmp1, tmp2))
#if(all.equal(tmp1, tmp2)){
# mpiunorm <- bind_rows(mpiunorm,
# tmp2 %>% mutate(norm="mediannorm"))
#}
#
##
## medianQuotientNorm
##
#tmp1 <- medianQuotientNorm(mw) %>%
# select(-normalization)
#
#tmp2 <- medianquotientnorm(mpiu) %>%
# spread(glycan, value)
#tmp2 <- data.frame(tmp2)
#
#print(all.equal(tmp1, tmp2))
#if(all.equal(tmp1, tmp2)){
# mpiunorm <- bind_rows(mpiunorm,
# tmp2 %>% mutate(norm="medianquotientnorm"))
#}
#
##
## quantileNorm
##
#library(preprocessCore)
#tmp1 <- quantileNorm(mw) %>%
# select(-normalization)
#
#tmp2 <- quantilenorm(mpiu, transpose=TRUE) %>%
# spread(glycan, value)
#tmp2 <- data.frame(tmp2)
#tmp2 <- tmp2[ , c(2,1,3:ncol(tmp2))]
#
#print(all.equal(tmp1, tmp2))
#if(all.equal(tmp1, tmp2)){
# mpiunorm <- bind_rows(mpiunorm,
# tmp2 %>% mutate(norm="quantilenormt"))
#}
#
#mpiunorm <- mpiunorm %>%
# gather(glycan, value, contains("GP")) %>%
# arrange(norm, Plate, gid, glycan)
#mpiunorm <- data.frame(mpiunorm)
#save(mpiunorm, file="./mpiunorm.RData")
#if(.Machine$sizeof.pointer==8){
#
# data(mpiu)
# data(mpiunorm)
#
#
# tanormdf <- mpiunorm %>%
# filter(norm=="tanorm") %>%
# select(-norm)
#
# refpeaknormdf <- mpiunorm %>%
# filter(norm=="refpeaknorm") %>%
# select(-norm)
#
# mediannormdf <- mpiunorm %>%
# filter(norm=="mediannorm") %>%
# select(-norm)
#
# medianquotientnormdf <- mpiunorm %>%
# filter(norm=="medianquotientnorm") %>%
# select(-norm)
#
# quantilenormtdf <- mpiunorm %>%
# filter(norm=="quantilenormt") %>%
# select(-norm)
#
# test_that("tanorm", {
# expect_equal(tanorm(mpiu), tanormdf)
# })
#
#
# test_that("refpeaknorm", {
# expect_equal(refpeaknorm(mpiu), refpeaknormdf)
# })
#
#
# test_that("mediannorm", {
# expect_equal(mediannorm(mpiu), mediannormdf)
# })
#
#
# test_that("medianquotientnorm", {
# expect_equal(medianquotientnorm(mpiu), medianquotientnormdf)
# })
# if(requireNamespace("preprocessCore", quietly=TRUE)){
# tmp <- quantilenorm(mpiu, transpose=TRUE)
# # reorder columns
# tmp <- tmp[, names(quantilenormtdf)] %>%
# arrange(Plate, gid, glycan)
#
# test_that("quantilenormt", {
# expect_equal(tmp, quantilenormtdf)
# })
# }
#}
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