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Merged
lgatto merged 1 commit into from
Sep 4, 2025
Merged

update make-data_krull2024.R #33

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11 changes: 6 additions & 5 deletions inst/scripts/make-data_krull2024.R
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,12 @@ root <- "~/localdata/SCP/krull2024/"

report <- read.delim(paste0(root, "report.tsv"))

## Correct the colname
report <- report %>%
rename(MS1.Area = Ms1.Area)
## Match file names with protein assay sample names
report$File.Name <- paste0("X", report$Run)

## Build the annotation table from the run names
annot <- DataFrame(File.Name = unique(report$File.Name))
annot$Run <- gsub("^D.*[\\]|[.]d$", "", annot$File.Name)
annot$Run <- sub("X", "", annot$File.Name)
otherVars <- strsplit(annot$Run, "_")
otherVars <- lapply(otherVars, function(x) {
if (length(x) == 12) x <- x[-4]
Expand All @@ -36,9 +35,11 @@ colnames(otherVars) <- c("Date", "..undetermined..", "SampleAnnotation",
"..undetermined..", "RunID")
annot <- cbind(annot, otherVars)
annot <- annot[, !grepl("\\.\\.undetermined\\.\\.", colnames(annot))]
rownames(annot) <- annot$File.Name

## Format to a QFeatures object
krull2024 <- readSCPfromDIANN(annot, report)
krull2024 <- readSCPfromDIANN(report)
colData(krull2024) <- annot

####---- Add the protein data ----####
## Data downloaded from:
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