diff --git a/R/converters.R b/R/converters.R index d52ec7c..50a638a 100644 --- a/R/converters.R +++ b/R/converters.R @@ -191,9 +191,9 @@ DIANNtoMSstatsPTMFormat = function(input, #' The probability is confidence score determined by PeptideProphet and higher values indicate greater confidence. #' @param useUniquePeptide logical, if TRUE (default) removes peptides that are assigned for more than one proteins. #' We assume to use unique peptide for each protein. -#' @param rmPSM_withfewMea_withinRun TRUE (default) will remove the features that have 1 or 2 measurements within each Run. +#' @param rmPSM_withfewMea_withinRun TRUE will remove the features that have 1 or 2 measurements within each Run. Default is FALSE. #' @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 summaryforMultipleRows 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 use_log_file logical. If TRUE, information about data processing will diff --git a/man/FragPipetoMSstatsPTMFormat.Rd b/man/FragPipetoMSstatsPTMFormat.Rd index 7c4c10c..af7589c 100644 --- a/man/FragPipetoMSstatsPTMFormat.Rd +++ b/man/FragPipetoMSstatsPTMFormat.Rd @@ -71,11 +71,11 @@ The probability is confidence score determined by PeptideProphet and higher valu \item{useUniquePeptide}{logical, if TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.} -\item{rmPSM_withfewMea_withinRun}{TRUE (default) will remove the features that have 1 or 2 measurements within each Run.} +\item{rmPSM_withfewMea_withinRun}{TRUE will remove the features that have 1 or 2 measurements within each Run. Default is FALSE.} \item{rmPeptide_OxidationM}{TRUE (default) will remove the peptides including oxidation (M) sequence.} -\item{rmProtein_with1Feature}{TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.} +\item{rmProtein_with1Feature}{TRUE will remove the proteins which have only 1 peptide and charge. Default is FALSE.} \item{summaryforMultipleRows}{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.}