Commit 051b75ef authored by Mathias Walzer's avatar Mathias Walzer
Browse files

added updates in rda files to R code - baseline

parent 7c0a66ea
......@@ -7,14 +7,14 @@ pxds <- c("PXD004873", "PXD000672", "PXD004691", "PXD014943", "PXD003497", "PXD0
for ( i in pxds ) {
data <- get(paste("ours_",i,sep=""))(norm="median") %>%
filter(feature_missingrate_per_group < 50) %>%
mutate(NormIntensities = `^`(2,NormLogIntensities)) %>%
select(-LogIntensities,-NormLogIntensities,-GROUP_ORIGINAL, -SUBJECT_ORIGINAL, -feature_missingrate_per_run, -feature_missingrate_per_group) %>%
select(-matches("technical_replicate"), -matches("sample_id"), -matches("sample_name")) %>%
spread(originalRUN, NormIntensities)
dplyr::filter(feature_missingrate_per_group < 50) %>%
dplyr::mutate(NormIntensities = `^`(2,NormLogIntensities)) %>%
dplyr::select(-LogIntensities,-NormLogIntensities,-GROUP_ORIGINAL, -SUBJECT_ORIGINAL, -feature_missingrate_per_run, -feature_missingrate_per_group) %>%
dplyr::select(-matches("technical_replicate"), -matches("sample_id"), -matches("sample_name")) %>%
tidyr::spread(originalRUN, NormIntensities)
write.table(data,
paste(i,"_baseline_mediannorm_untransformed.tsv",sep=""),
paste(i,"_baseline_mediannorm_untransformed_top3.tsv",sep=""),
quote = FALSE,
sep = "\t",
row.names = F)
......
......@@ -3,7 +3,7 @@ library(stringr)
# PXD014943
theirs_PXD014943 <- function(){
annot <- read.delim("../inputs/annotations/PXD014943_annotation_corrected.txt")
annot <- read.delim("../inputs/annotations/PXD014943_annotation_corrected_norecalc.txt")
ori <- read.delim("../inputs/original_results_from_supplementaries/PXD014943_suppl_protein_quant_samplelevel_only.tsv") %>%
dplyr::mutate(Protein = as.factor(Protein)) %>%
filter(across(Protein, ~ !grepl(';', .))) %>%
......
......@@ -23,7 +23,7 @@ source("../container/downstream/DIA_downstream_datacarpentry.R")
# PXD014194
ours_PXD014194 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD014194_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1/PXD014194_corrected.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD014194.rda"
load(rda)
if(missing(groups)) {
......@@ -47,7 +47,7 @@ ours_PXD014194 <- function(groups, norm="median"){
# PXD010912
ours_PXD010912 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD010912_annotation.txt")
rda <- "../inputs/rdas/fdr1/PXD010912.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD010912.rda"
load(rda)
if(missing(groups)) {
......@@ -71,7 +71,7 @@ ours_PXD010912 <- function(groups, norm="median"){
# PXD004873
ours_PXD004873 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD004873_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1/PXD004873_corrected.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD004873.rda"
load(rda)
if(missing(groups)) {
......@@ -96,7 +96,7 @@ ours_PXD004873 <- function(groups, norm="median"){
ours_PXD004691 <- function(groups, norm="median"){
# annot <- read.delim("../inputs/annotations/PXD004691_annotation.txt") %>% dplyr::select(Run,Condition,BioReplicate,technical_replicate,sample_name)
annot <- read.delim("../inputs/annotations/PXD004691_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1/PXD004691_corrected.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD004691.rda"
load(rda)
if(missing(groups)) {
......@@ -120,7 +120,7 @@ ours_PXD004691 <- function(groups, norm="median"){
# PXD004589
ours_PXD004589 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD004589_annotation.txt")
rda <- "../inputs/rdas/fdr1/PXD004589.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD004589.rda"
load(rda)
if(missing(groups)) {
......@@ -144,7 +144,7 @@ ours_PXD004589 <- function(groups, norm="median"){
# PXD003497
ours_PXD003497 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD003497_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1/PXD003497_corrected.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD003497.rda"
load(rda)
if(missing(groups)) {
......@@ -171,7 +171,7 @@ ours_PXD000672 <- function(groups, norm="median"){
# annot <- read.delim("../inputs/annotations/PXD000672_annotation.txt")
# rda <- "../inputs/rdas/fdr1/PXD000672.rda"
annot <- read.delim("../inputs/annotations/PXD000672_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1/PXD000672_corrected.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD000672.rda"
load(rda)
if(missing(groups)) {
......@@ -196,7 +196,7 @@ ours_PXD000672 <- function(groups, norm="median"){
# PXD001064
ours_PXD001064 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD001064_serum_annotation.txt")
rda <- "../inputs/rdas/fdr1/PXD001064_serum.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD001064_serum.rda"
load(rda)
if(missing(groups)) {
......@@ -220,7 +220,7 @@ ours_PXD001064 <- function(groups, norm="median"){
# PXD003539
ours_PXD003539 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD003539_annotation.txt")
rda <- "../inputs/rdas/fdr1/PXD003539.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD003539.rda"
load(rda)
if(missing(groups)) {
......@@ -244,7 +244,7 @@ ours_PXD003539 <- function(groups, norm="median"){
# PXD014943
ours_PXD014943 <- function(groups, norm="median"){
annot <- read.delim("../inputs/annotations/PXD014943_annotation_corrected_norecalc.txt")
rda <- "../inputs/rdas/fdr1/PXD014943.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD014943.rda"
load(rda)
if(missing(groups)) {
......@@ -268,7 +268,7 @@ ours_PXD014943 <- function(groups, norm="median"){
# PXD000
ours_test <- function(diff, groups, norm="median") {
annot <- read.delim("../inputs/annotations/PXD014943_annotation_corrected_norecalc.txt")
rda <- "../inputs/rdas/fdr1/PXD014943.rda"
rda <- "../inputs/rdas/fdr1_top3_inference/PXD014943.rda"
load(rda)
if(missing(groups)) {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment