From ac2e5c0d3a5872dbf50ace5d08236516e4100d6f Mon Sep 17 00:00:00 2001 From: tonywu1999 Date: Wed, 14 May 2025 09:56:25 -0400 Subject: [PATCH] Add description in DIANN converter on DIANN 2.0 workaround --- R/converters_DIANNtoMSstatsFormat.R | 4 +++- man/DIANNtoMSstatsFormat.Rd | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R index 1d331574..df3c4bd7 100644 --- a/R/converters_DIANNtoMSstatsFormat.R +++ b/R/converters_DIANNtoMSstatsFormat.R @@ -1,7 +1,8 @@ #' Import Diann files #' #' @inheritParams .sharedParametersAmongConverters -#' @param input name of MSstats input report from Diann, which includes feature-level data. +#' @param input name of MSstats input report from Diann, which includes fragment-level data. +#' Output fragment data with --export-quant flag in DIA-NN 2.0 #' @param annotation name of 'annotation.txt' data which includes Condition, BioReplicate, Run. #' @param MBR True if analysis was done with match between runs #' @param global_qvalue_cutoff The qvalue cutoff for the Q.Value column, i.e. @@ -29,6 +30,7 @@ #' @export #' #' @examples +#' # See https://github.com/vdemichev/DiaNN/discussions/1525 for workaround for DIANN 2.0 #' input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", #' package="MSstatsConvert") #' annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd index 659692a3..f7c2a68c 100644 --- a/man/DIANNtoMSstatsFormat.Rd +++ b/man/DIANNtoMSstatsFormat.Rd @@ -24,7 +24,8 @@ DIANNtoMSstatsFormat( ) } \arguments{ -\item{input}{name of MSstats input report from Diann, which includes feature-level data.} +\item{input}{name of MSstats input report from Diann, which includes fragment-level data. +Output fragment data with --export-quant flag in DIA-NN 2.0} \item{annotation}{name of 'annotation.txt' data which includes Condition, BioReplicate, Run.} @@ -77,6 +78,7 @@ data.frame in the MSstats required format. Import Diann files } \examples{ +# See https://github.com/vdemichev/DiaNN/discussions/1525 for workaround for DIANN 2.0 input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", package="MSstatsConvert") annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv",