From 4f59dcdad0e0e8877f8aa601fde19dda3863d61e Mon Sep 17 00:00:00 2001 From: Christophe Vanderaa Date: Thu, 22 Jun 2023 10:46:35 +0200 Subject: [PATCH] docs: documented missing argument --- R/readSCP.R | 5 ++++- man/readSCPfromDIANN.Rd | 3 +++ man/readSingleCellExperiment.Rd | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/R/readSCP.R b/R/readSCP.R index d017e6a..0380f96 100644 --- a/R/readSCP.R +++ b/R/readSCP.R @@ -167,7 +167,7 @@ readSCP <- function(featureData, colData, batchCol, channelCol, ##' the column names are composed of special characters like `(` ##' or `-` that will be converted to a `.` by the `read.csv` ##' function. If `ecol` does not match, the error message will -##' dislpay the column names as seen by the `read.csv` function. +##' display the column names as seen by the `read.csv` function. ##' ##' @param fnames An optional `character(1)` or `numeric(1)` ##' indicating the column to be used as row names. @@ -240,6 +240,9 @@ readSingleCellExperiment <- function(table, ##' file generated by DIA-NN. This argument is optional and is ##' only applicable for mulitplixed experiments ##' +##' @param ecol A `character(1)` indicating which column in +##' `reportData` contains the quantitative information. +##' ##' @param multiplexing A `character(1)` indicating the type of ##' multiplexing used in the experiment. Provide `"none"` if the ##' experiment is label-free (default). Available options are: diff --git a/man/readSCPfromDIANN.Rd b/man/readSCPfromDIANN.Rd index 8716c31..51fa56e 100644 --- a/man/readSCPfromDIANN.Rd +++ b/man/readSCPfromDIANN.Rd @@ -33,6 +33,9 @@ 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} +\item{ecol}{A \code{character(1)} indicating which column in +\code{reportData} contains the quantitative information.} + \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: diff --git a/man/readSingleCellExperiment.Rd b/man/readSingleCellExperiment.Rd index 222fd19..0ca56e7 100644 --- a/man/readSingleCellExperiment.Rd +++ b/man/readSingleCellExperiment.Rd @@ -19,7 +19,7 @@ indicating the names of the columns. Caution must be taken if the column names are composed of special characters like \code{(} or \code{-} that will be converted to a \code{.} by the \code{read.csv} function. If \code{ecol} does not match, the error message will -dislpay the column names as seen by the \code{read.csv} function.} +display the column names as seen by the \code{read.csv} function.} \item{fnames}{An optional \code{character(1)} or \code{numeric(1)} indicating the column to be used as row names.}