From 1bf49df634ee2ee03f1c4a39e577b2aba03eb1a6 Mon Sep 17 00:00:00 2001
From: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: Fri, 8 Mar 2024 23:48:39 +0100
Subject: [PATCH] fix codoc error

---
 R/QFeatures-constructors.R    |  4 ++--
 man/readQFeaturesFromDIANN.Rd | 11 ++++++-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/R/QFeatures-constructors.R b/R/QFeatures-constructors.R
index a37f1cdd..4d3bdbdf 100644
--- a/R/QFeatures-constructors.R
+++ b/R/QFeatures-constructors.R
@@ -398,7 +398,7 @@ QFeatures <- function(..., assayLinks = NULL) {
 ##'
 ##' @param ecol A `character(1)` indicating which column in
 ##'     `reportData` contains the quantitative information. Default is
-##'     `"MS1.Area"`.
+##'     `"Ms1.Area"`.
 ##'
 ##' @param multiplexing A `character(1)` indicating the type of
 ##'     multiplexing used in the experiment. Provide `"none"` if the
@@ -430,7 +430,7 @@ QFeatures <- function(..., assayLinks = NULL) {
 ##' ## fix file names
 ##' x[[1]] <- sub("^.+raw-data\\\\", "", x[[1]])
 ##' cd <- data.frame(File.Name = unique(x[[1]]))
-##' readQFeaturesFromDIANN(colData = cd, reportData = x, ecol = "Ms1.Area")
+##' readQFeaturesFromDIANN(colData = cd, reportData = x)
 readQFeaturesFromDIANN <- function(colData, reportData, extractedData = NULL,
                                    ecol = "Ms1.Area", multiplexing = "none",
                                    ...) {
diff --git a/man/readQFeaturesFromDIANN.Rd b/man/readQFeaturesFromDIANN.Rd
index 35b602bc..eb5a090e 100644
--- a/man/readQFeaturesFromDIANN.Rd
+++ b/man/readQFeaturesFromDIANN.Rd
@@ -8,7 +8,7 @@ readQFeaturesFromDIANN(
   colData,
   reportData,
   extractedData = NULL,
-  ecol = "MS1.Area",
+  ecol = "Ms1.Area",
   multiplexing = "none",
   ...
 )
@@ -29,15 +29,16 @@ file generated by DIA-NN.}
 \item{extractedData}{A data.frame or any object that can be coerced
 to a data.frame that contains the data from the \verb{*_ms1_extracted.tsv}
 file generated by DIA-NN. This argument is optional and is
-only applicable for mulitplixed experiments}
+currently only applicable for mTRAQ multiplexed experiments
+where DIA-NN was run using the \code{plexdia} module.}
 
 \item{ecol}{A \code{character(1)} indicating which column in
 \code{reportData} contains the quantitative information. Default is
-\code{"MS1.Area"}.}
+\code{"Ms1.Area"}.}
 
 \item{multiplexing}{A \code{character(1)} indicating the type of
 multiplexing used in the experiment. Provide \code{"none"} if the
-experiment is label-free (default). Available options are:
+experiment is label-free (default). Alternative options are:
 \code{"mTRAQ"}.}
 
 \item{...}{Further arguments passed to \code{\link[=readQFeatures]{readQFeatures()}}.}
@@ -63,7 +64,7 @@ x <- read.delim(MsDataHub::benchmarkingDIA.tsv())
 ## fix file names
 x[[1]] <- sub("^.+raw-data\\\\\\\\", "", x[[1]])
 cd <- data.frame(File.Name = unique(x[[1]]))
-readQFeaturesFromDIANN(colData = cd, reportData = x, ecol = "Ms1.Area")
+readQFeaturesFromDIANN(colData = cd, reportData = x)
 }
 \author{
 Laurent Gatto, Christophe Vanderaa