Tweak set of MQ XML return values

fmicompbio · Jul 17, 2023 · 59282f4 · 59282f4
1 parent 194cad8
commit 59282f4
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Showing 2 changed files with 2 additions and 6 deletions.
diff --git a/R/readMaxQuantXML.R b/R/readMaxQuantXML.R
@@ -98,10 +98,8 @@ readMaxQuantXML <- function(mqParameterFile) {
             "Sample names" = mq_experiments,
             "Databases" = mq_fasta_files,
             "Contaminants" = mq_contaminants,
-            "Quantification mode" = mq_quant_mode,
             "Quantification settings (LFQ)" = mq_quant_methods,
             "Min. razor peptides" = mq_peptides_for_quantification,
-            "Requantify" = mq_requantify,
             "Enzymes" = mq_enzymes,
             "Variable modifications" = mq_variable_modifications,
             "Fixed modifications" = mq_fixed_modifications,

diff --git a/tests/testthat/test-readMaxQuantXML.R b/tests/testthat/test-readMaxQuantXML.R
@@ -17,9 +17,9 @@ test_that("reading MQ XML file works", {
     expect_equal(length(mq), 17)
     expect_named(mq, c("MaxQuant version", "Parameter file", "Search engine",
                        "Raw file location", "Raw files", "Sample names",
-                       "Databases", "Contaminants", "Quantification mode",
+                       "Databases", "Contaminants",
                        "Quantification settings (LFQ)", "Min. razor peptides",
-                       "Requantify", "Enzymes", "Variable modifications",
+                       "Enzymes", "Variable modifications",
                        "Fixed modifications", "Max peptide mass",
                        "Min peptide length"))
 
@@ -29,11 +29,9 @@ test_that("reading MQ XML file works", {
     ## Check individual values
     expect_equal(mq$`MaxQuant version`, "1.5.3.8")
     expect_equal(mq$`Sample names`, "Adnp_IP04, Adnp_IP05, Adnp_IP06, Chd4BF_IP07, Chd4BF_IP08, Chd4BF_IP09, RBC_ctrl_IP01, RBC_ctrl_IP02, RBC_ctrl_IP03")
-    expect_equal(mq$`Quantification mode`, "1")
     expect_equal(mq$`Quantification settings (LFQ)`,
                  "LFQ min. ratio count: 1, fastLFQ: false, match-between runs (MBR): true, Intensity based absolute quantification (iBAQ): true")
     expect_equal(mq$`Min. razor peptides`, "1")
-    expect_equal(mq$Requantify, "false")
     expect_equal(mq$Enzymes, "Trypsin/P")
     expect_equal(mq$`Variable modifications`, "Oxidation (M), Acetyl (Protein N-term)")
     expect_equal(mq$`Fixed modifications`, "")