docs(fractions): Update documentation around fractionation (#136)

Author: tonywu1999

DESCRIPTION

@@ -14,7 +14,6 @@ License: Artistic-2.0
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 biocViews: MassSpectrometry, Proteomics, Software, DataImport, QualityControl
 Depends:
     R (>= 4.0)
@@ -82,3 +81,4 @@ Collate:
     'utils_logging.R'
     'utils_shared_peptides.R'
 VignetteBuilder: knitr
+Config/roxygen2/version: 8.0.0

R/utils_documentation.R

@@ -5,7 +5,11 @@
 #' @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 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 summaryforMultipleRows max or sum - when multiple PSMs identify
+#' the same feature within a single MS run (duplicate PSMs), use the
+#' highest (max) or sum of the duplicate intensities. Default is max for
+#' label-free converters and sum for TMT converters. Note that this parameter 
+#' does NOT control collapsing across fractions of the same biological mixture.
 #' @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.