derks2022: updated broken links

inst/scripts/make-data_derks2022.R

@@ -9,6 +9,7 @@ datadir <- "~/PhD/.localdata/SCP/derks2022/"
 
 ## Sample annotations
 
+
 sampleAnnot <- read.delim(paste0(datadir, "Meta_SingleCell_updated_1.tsv"))
 ## Add which dataset each sample is part of
 sampleAnnot$dataset <- sampleAnnot$Instrument
@@ -24,6 +25,8 @@ sampleAnnot$File.Name <- ifelse(sampleAnnot$Instrument == "timsTOFSCP",
 
 ## Bulk data
 
+## cf https://drive.google.com/drive/folders/1yRzuIXnMbt-_8_skOgiVkJksqc20RoLK
+
 # We load the DIA-NN main output table and the MS1 extracted report table.
 # These are read and combined in a `QFeatures`object. 
 extractedDataBulk <- read.delim(paste0(datadir, "qe_bulk/Report.pr_matrix_channels_ms1_extracted.tsv"))
@@ -38,6 +41,8 @@ names(bulk)[length(bulk)] <- "bulk_prec_extracted"
 
 ## Load timsTOF-SCP data
 
+## cf https://drive.google.com/drive/folders/1RosRkMdYfhbQ-XtUNKly0TdCrZrUQVmO
+
 # We load the DIA-NN main output table and the MS1 extracted report table.
 # These are read and combined in a `QFeatures`object. 
 extractedDataTims <- read.delim(paste0(datadir, "tims_sc/Report.pr_matrix_channels_ms1_extracted.tsv"))
@@ -53,6 +58,8 @@ names(tims)[length(tims)] <- "tims_prec_extracted"
 
 ## Load Q-Exactive data
 
+## cf https://drive.google.com/drive/folders/1b_pavZ2sufR3oYBy2z9fVepCRDKXGvyF
+
 # We load the DIA-NN main output table and the MS1 extracted report table.
 # These are read and combined in a `QFeatures`object. 
 extractedDataQE <- read.delim(paste0(datadir, "qe_sc/Report.pr_matrix_channels_ms1_extracted.tsv"))