fix docs

Author: tonywu1999

R/converters_MaxQtoMSstatsTMTFormat.R

@@ -6,7 +6,7 @@
 #' @param which.proteinid Use 'Proteins' (default) column for protein name. 'Leading.proteins' or 'Leading.razor.proteins' or 'Gene.names' can be used instead to get the protein ID with single protein. However, those can potentially have the shared peptides.
 #' @param rmProt_Only.identified.by.site TRUE will remove proteins with '+' in 'Only.identified.by.site' column from proteinGroups.txt, which was identified only by a modification site. FALSE is the default.
 #' @param rmPSM_withfewMea_withinRun TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
-#' @param rmProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
+#' @param rmProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Default is FALSE.
 #' @param ... additional parameters to `data.table::fread`.
 #' @inheritParams .sharedParametersAmongConverters
 #' 

R/converters_OpenMStoMSstatsTMTFormat.R

@@ -1,7 +1,7 @@
 #' Generate MSstatsTMT required input format for OpenMS output
 #' @param input MSstatsTMT report from OpenMS
 #' @param rmPSM_withfewMea_withinRun TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
-#' @param rmProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
+#' @param rmProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Default is FALSE.
 #' @param summaryforMultiplePSMs sum(default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.
 #' @param ... additional parameters to `data.table::fread`.
 #' @inheritParams .sharedParametersAmongConverters

R/converters_PhilosophertoMSstatsTMTFormat.R

@@ -13,7 +13,7 @@
 #' The probability is confidence score determined by PeptideProphet and higher values indicate greater confidence.
 #' @param rmPSM_withfewMea_withinRun TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
 #' @param rmPeptide_OxidationM TRUE (default) will remove the peptides including oxidation (M) sequence.
-#' @param rmProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
+#' @param rmProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Default is FALSE.
 #' @param ... additional parameters to `data.table::fread`.
 #' @inheritParams .sharedParametersAmongConverters
 #' 
@@ -102,7 +102,9 @@ PhilosophertoMSstatsTMTFormat = function(
 
 
 #' Convert Philosopher parameters to consistent format
-#' @inheritParams PhilosophertoMSstatsTMTFormat 
+#' @inheritParams PhilosophertoMSstatsTMTFormat
+#' @param path character. Path to a file or directory containing msstats.csv output(s) from Philosopher. Used when \code{input} is NULL.
+#' @param folder logical. If TRUE, \code{path} is treated as a directory and all msstats files within it are read. If FALSE, \code{path} is treated as a single file path.
 #' @keywords internal
 .getPhilosopherInput = function(input, path, folder) {
     if (!is.null(input)) {

R/utils_documentation.R

@@ -5,7 +5,7 @@
 #' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements across runs.
 #' @param useUniquePeptide TRUE (default) removes peptides that are assigned for more than one proteins. 
 #' We assume to use unique peptide for each protein.
-#' @param summaryforMultipleRows max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
+#' @param summaryforMultipleRows max or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities. Default is max for label-free converters and sum for TMT converters.
 #' @param removeProtein_with1Feature TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
 #' @param removeProtein_with1Peptide TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
 #' @param removeOxidationMpeptides TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
@@ -14,7 +14,7 @@
 #' will be saved to a file.
 #' @param append logical. If TRUE, information about data processing will be added
 #' to an existing log file.
-#' @param verbose logical. If TRUE, information about data processing wil be printed
+#' @param verbose logical. If TRUE, information about data processing will be printed
 #' to the console.
 #' @param log_file_path character. Path to a file to which information about 
 #' data processing will be saved. 

inst/tinytest/test_converters_PDtoMSstatsTMTFormat.R

@@ -24,10 +24,11 @@ annotation.pd = data.table::fread(system.file("tinytest/raw_data/PDTMT/pd_annota
                                               package = "MSstatsConvert"))
 
 expect_error(PDtoMSstatsTMTFormat(input = pd_raw[, !colnames(pd_raw) == "Protein.Accessions"], # missing columns in input
-                                  annotation = annot))
+                                  annotation = annot, use_log_file = FALSE))
 
 expect_error(PDtoMSstatsTMTFormat(input = pd_raw,
-                                  annotation = annot[, !colnames(annot) == "Condition"])) # missing columns in annotation
+                                  annotation = annot[, !colnames(annot) == "Condition"], # missing columns in annotation
+                                  use_log_file = FALSE))
 
 # Verify output intensities are present in input
 intensity_cols = grep("^Abundance", colnames(pd_raw), value = TRUE)