docs(getSubnetworkFromIndra): Switch MSstats as dependency, adjust li…

…nk to groupComparison (#22)

* docs(getSubnetworkFromIndra): Switch MSstats as dependency, add link to groupComparison

* update manual for visualizeNetworks

DESCRIPTION

@@ -20,15 +20,15 @@ Imports:
     RCy3,
     httr,
     jsonlite,
-    r2r
+    r2r,
+    MSstats
 Suggests: 
     data.table,
     BiocStyle,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
     mockery,
-    MSstats,
     MSstatsConvert
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, 

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
 #'