diff --git a/R/clean_MaxQuant.R b/R/clean_MaxQuant.R index 3c3784df..2c11040c 100644 --- a/R/clean_MaxQuant.R +++ b/R/clean_MaxQuant.R @@ -17,12 +17,12 @@ mq_input = getInputFile(msstats_object, "evidence") mq_pg = getInputFile(msstats_object, "protein_groups") - filter_cols = c("Contaminant", "Potentialcontaminant", "Reverse") - msg = paste("** + Contaminant, + Reverse, + Potential.contaminant", + filter_cols = c("Contaminant", "Potentialcontaminant", "Reverse", "Decoy") + msg = paste("** + Contaminant, + Reverse, + Decoy, + Potential.contaminant", "proteins are removed.") if (remove_by_site) { filter_cols = c(filter_cols, "Onlyidentifiedbysite") - msg = paste("** + Contaminant, + Reverse, + Potential.contaminant,", + msg = paste("** + Contaminant, + Reverse, + Decoy, + Potential.contaminant,", "+ Only.identified.by.site proteins are removed.") }