diff --git a/DESCRIPTION b/DESCRIPTION index 8105f73..c34fdd8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,7 +20,8 @@ Imports: RCy3, httr, jsonlite, - r2r + r2r, + MSstats Suggests: data.table, BiocStyle, @@ -28,7 +29,6 @@ Suggests: rmarkdown, testthat (>= 3.0.0), mockery, - MSstats, MSstatsConvert VignetteBuilder: knitr biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, diff --git a/R/getSubnetworkFromIndra.R b/R/getSubnetworkFromIndra.R index 4d60492..7c20dda 100644 --- a/R/getSubnetworkFromIndra.R +++ b/R/getSubnetworkFromIndra.R @@ -3,14 +3,14 @@ #' Using differential abundance results from MSstats, this function retrieves #' a subnetwork of protein interactions from INDRA database. #' -#' @param input output of groupComparison function's comparisionResult table, -#' which contains a list of proteins and their corresponding p-values, logFCs, -#' along with additional HGNC ID and HGNC name columns +#' @param input output of \code{\link[MSstats]{groupComparison}} function's +#' comparisionResult table, which contains a list of proteins and their +#' corresponding p-values, logFCs, along with additional HGNC ID and HGNC +#' name columns #' @param pvalueCutoff p-value cutoff for filtering. Default is NULL, i.e. no #' filtering #' #' @return list of 2 data.frames, nodes and edges -#' @seealso \code{\link[MSstats]{groupComparison}} #' #' @export #' diff --git a/man/getSubnetworkFromIndra.Rd b/man/getSubnetworkFromIndra.Rd index ca46bff..2f5ed5b 100644 --- a/man/getSubnetworkFromIndra.Rd +++ b/man/getSubnetworkFromIndra.Rd @@ -7,9 +7,10 @@ getSubnetworkFromIndra(input, pvalueCutoff = NULL) } \arguments{ -\item{input}{output of groupComparison function's comparisionResult table, -which contains a list of proteins and their corresponding p-values, logFCs, -along with additional HGNC ID and HGNC name columns} +\item{input}{output of \code{\link[MSstats]{groupComparison}} function's +comparisionResult table, which contains a list of proteins and their +corresponding p-values, logFCs, along with additional HGNC ID and HGNC +name columns} \item{pvalueCutoff}{p-value cutoff for filtering. Default is NULL, i.e. no filtering} @@ -31,6 +32,3 @@ head(subnetwork$nodes) head(subnetwork$edges) } -\seealso{ -\code{\link[MSstats]{groupComparison}} -}