Commit d0918a15 authored by Mathias Walzer's avatar Mathias Walzer
Browse files

fixed intermediate results availability and documentation

parent 15256871
......@@ -51,7 +51,7 @@ tally_protpepirt <- function(rda, annot) {
# PXD014194
ours_PXD014194 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD014194_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD014194.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD014194.rda"
load(rda)
if(missing(groups)) {
......@@ -86,7 +86,7 @@ ours_PXD014194 <- function(groups, norm="median", tally=FALSE){
# PXD010912
ours_PXD010912 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD010912_annotation.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD010912.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD010912.rda"
load(rda)
if(missing(groups)) {
......@@ -121,7 +121,7 @@ ours_PXD010912 <- function(groups, norm="median", tally=FALSE){
# PXD004873
ours_PXD004873 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD004873_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD004873.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD004873.rda"
load(rda)
if(missing(groups)) {
......@@ -157,7 +157,7 @@ ours_PXD004873 <- function(groups, norm="median", tally=FALSE){
ours_PXD004691 <- function(groups, norm="median", tally=FALSE){
# 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_top3_inference/PXD004691.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD004691.rda"
load(rda)
if(missing(groups)) {
......@@ -192,7 +192,7 @@ ours_PXD004691 <- function(groups, norm="median", tally=FALSE){
# PXD004589
ours_PXD004589 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD004589_annotation.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD004589.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD004589.rda"
load(rda)
if(missing(groups)) {
......@@ -227,7 +227,7 @@ ours_PXD004589 <- function(groups, norm="median", tally=FALSE){
# PXD003497
ours_PXD003497 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD003497_annotation_corrected.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD003497.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD003497.rda"
load(rda)
if(missing(groups)) {
......@@ -265,7 +265,7 @@ ours_PXD000672 <- function(groups, norm="median", tally=FALSE){
# 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_top3_inference/PXD000672.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD000672.rda"
load(rda)
if(missing(groups)) {
......@@ -301,7 +301,7 @@ ours_PXD000672 <- function(groups, norm="median", tally=FALSE){
# PXD001064
ours_PXD001064 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD001064_serum_annotation.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD001064_serum.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD001064_serum.rda"
load(rda)
if(missing(groups)) {
......@@ -336,7 +336,7 @@ ours_PXD001064 <- function(groups, norm="median", tally=FALSE){
# PXD003539
ours_PXD003539 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD003539_annotation.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD003539.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD003539.rda"
load(rda)
if(missing(groups)) {
......@@ -371,7 +371,7 @@ ours_PXD003539 <- function(groups, norm="median", tally=FALSE){
# PXD014943
ours_PXD014943 <- function(groups, norm="median", tally=FALSE){
annot <- read.delim("../inputs/annotations/PXD014943_annotation_corrected_norecalc.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD014943.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD014943.rda"
load(rda)
if(missing(groups)) {
......@@ -406,7 +406,7 @@ ours_PXD014943 <- function(groups, norm="median", tally=FALSE){
# PXD000
ours_test <- function(diff, groups, norm="median") {
annot <- read.delim("../inputs/annotations/PXD014943_annotation_corrected_norecalc.txt")
rda <- "../inputs/rdas/fdr1_top3_inference/PXD014943.rda"
rda <- "../inputs/intermediate-results/msstats_rdas/fdr1_top3_inference/PXD014943.rda"
load(rda)
if(missing(groups)) {
......
# DIA reanalysis
This folder contains various configuration examples and inputs (which might in turn be outputs, i.e. intermediate results of the pipeline).
Target library inputs can be found in [libs/](libs/), nextflow configuration files in [configs/](configs/), annotations for downstream processing in [annotations/](annotations/), downstream result files for post-processing in [rdas/](rdas/).
Target library inputs can be found in [libs/](libs/),
nextflow configuration files in [configs/](configs/),
annotations for downstream processing in [annotations/](annotations/),
downstream intermedidate result files for the reanalysis of the first 10 datasets can be found in the table below.
In order to integrate with the reanalysis code, please make sure to place the files in their target folders after download.
For convenience, we prepared batch download files in the respective folders ([intermediate-results/tric_tsvs](intermediate-results/tric_tsvs) and [intermediate-results/msstats_rdas](intermediate-results/msstats_rdas) ).
| Project | TRIC results URL | MSstats results URL |
|----------|:-------------------:|:------------------------:|
| PXD000672 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD000672.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD000672.rda |
| PXD001064 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD001064.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD001064_serum.rda |
| PXD003497 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD003497.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD003497.rda |
| PXD003539 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD003539.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD003539.rda |
| PXD004589 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD004589.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD004589.rda |
| PXD004691 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD004691.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD004691.rda |
| PXD004873 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD004873.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD004873.rda |
| PXD010912 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD010912.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD010912.rda |
| PXD014194 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD014194.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD014194.rda |
| PXD014943 | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD014943.tric.tsv.tar.gz | https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD014943.rda |
#!/usr/bin/env bash
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD000672.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD001064_serum.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD003497.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD003539.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD004589.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD004691.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD004873.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD010912.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD014194.rda'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/msstats_rdas/PXD014943.rda'
\ No newline at end of file
#!/usr/bin/env bash
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD000672.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD001064.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD003497.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD003539.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD004589.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD004691.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD004873.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD010912.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD014194.tric.tsv.tar.gz'
curl -O -J 'https://uk1s3.embassy.ebi.ac.uk/DIA-reanalysis/intermediate-results/tric_tsvs/PXD014943.tric.tsv.tar.gz'
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