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Hotfix/v2.7.1 to develop #113

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888db03
Merge pull request #100 from UMCUGenetics/develop
mraves2 Mar 20, 2026
b08f5e9
Merge pull request #102 from UMCUGenetics/develop
mraves2 Mar 20, 2026
e1baa76
Merge pull request #106 from UMCUGenetics/develop
mraves2 Mar 23, 2026
f29294e
Merge pull request #111 from UMCUGenetics/develop
mraves2 Mar 27, 2026
7698698
Merge pull request #101 from UMCUGenetics/release/v2.7.0
mraves2 Mar 27, 2026
4d1fa2c
fixed bug in filtered replication_pattern in DIMS/EvaluateTICs.R
mraves2 Apr 2, 2026
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8 changes: 5 additions & 3 deletions DIMS/EvaluateTics.R
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Expand Up @@ -44,15 +44,17 @@ print(remove_tech_reps)
remove_neg <- remove_tech_reps$neg
repl_pattern_filtered <- remove_from_repl_pattern(remove_neg, repl_pattern, nr_replicates)
save(repl_pattern_filtered, file = "negative_repl_pattern.RData")
# get an overview of suitable technical replicates for both negative mode
allsamples_techreps_neg <- get_overview_tech_reps(repl_pattern_filtered, "negative")

# positive scan mode
remove_pos <- remove_tech_reps$pos
repl_pattern_filtered <- remove_from_repl_pattern(remove_pos, repl_pattern, nr_replicates)
save(repl_pattern_filtered, file = "positive_repl_pattern.RData")

# get an overview of suitable technical replicates for both scan modes
allsamples_techreps_neg <- get_overview_tech_reps(repl_pattern_filtered, "negative")
# get an overview of suitable technical replicates for positive scan mode
allsamples_techreps_pos <- get_overview_tech_reps(repl_pattern_filtered, "positive")

# get an overview of suitable technical replicates for both scan modes and save to file
allsamples_techreps_both_scanmodes <- rbind(allsamples_techreps_pos, allsamples_techreps_neg)
write.table(allsamples_techreps_both_scanmodes,
file = "replicates_per_sample.txt",
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