From c94f3d2a28bc6408edc56acb8502386089ffd451 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dcallan@upenn.edu>
Date: Thu, 25 Apr 2024 23:24:40 -0400
Subject: [PATCH] clean up correlation coef and pvalue filtering helpers

---
 R/methods-CorrelationNetwork.R | 32 +++++++++++++-------------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/R/methods-CorrelationNetwork.R b/R/methods-CorrelationNetwork.R
index 730ff9a..ce8dd9a 100644
--- a/R/methods-CorrelationNetwork.R
+++ b/R/methods-CorrelationNetwork.R
@@ -5,49 +5,43 @@ setMethod("getCorrelationCoefThreshold", "CorrelationNetwork", function(object)
 setGeneric("getPValueThreshold", function(object) standardGeneric("getPValueThreshold"))
 setMethod("getPValueThreshold", "CorrelationNetwork", function(object) object@pValueThreshold)
 
-
-#' @include methods-CorrelationLinks.R
-linkAboveCorrelationCoefThreshold <- function(link, threshold) {
-  return(abs(correlationCoef(link)) >= threshold)
-}
-
 #' Prune Links by Correlation Coefficient
 #' 
 #' Removes links that have an absolute correlation coefficient below a
-#' threshold. This is a convenience function that calls pruneLinksByPredicate.
+#' threshold. This is a convenience function that calls pruneCorrelationLinks.
 #' @param net A CorrelationNetwork object
 #' @param correlationCoefThreshold The threshold
 #' @param verbose If TRUE, will print messages
 #' @export
-pruneLinksByCorrelationCoef <- function(net, correlationCoefThreshold, verbose = c(TRUE, FALSE)) {
+pruneLinksByCorrelationCoef <- function(net, correlationCoefThreshold = NULL, verbose = c(TRUE, FALSE)) {
   verbose <- veupathUtils::matchArg(verbose)
 
-  return(pruneLinksByPredicate(net = net, predicate = linkAboveCorrelationCoefThreshold, threshold = correlationCoefThreshold, verbose = verbose))
-}
-
-
-linkBelowPValueThreshold <- function(link, threshold) {
-  return(pValue(link) <= threshold)
+  return(pruneCorrelationLinks(net = net, correlationCoefThreshold = correlationCoefThreshold, verbose = verbose))
 }
 
 #' Prune Links by P-Value
 #' 
 #' Removes links that have a p-value above a threshold. This is a convenience
-#' function that calls pruneLinksByPredicate.
+#' function that calls pruneCorrelationLinks.
 #' @param net A Network object
 #' @param pValueThreshold The threshold
 #' @param verbose If TRUE, will print messages
 #' @export
-pruneLinksBelowWeight <- function(net, threshold, verbose = c(TRUE, FALSE)) {
+pruneLinksByPValue <- function(net, pValueThreshold = NULL, verbose = c(TRUE, FALSE)) {
   verbose <- veupathUtils::matchArg(verbose)
 
-  return(pruneLinksByPredicate(net = net, predicate = linkBelowPValueThreshold, threshold = pValueThreshold, verbose = verbose))
+  return(pruneCorrelationLinks(net = net, pValueThreshold = pValueThreshold, verbose = verbose))
 }
 
 #' @rdname pruneCorrelationLinks
 #' @aliases pruneCorrelationLinks,CorrelationNetwork-method
-setMethod("pruneCorrelationLinks", "CorrelationNetwork", function(object, correlationCoefThreshold, pValueThreshold, verbose = c(TRUE, FALSE)) {
-
+setMethod("pruneCorrelationLinks", "CorrelationNetwork", 
+function(
+  object, 
+  correlationCoefThreshold = NULL, 
+  pValueThreshold = NULL, 
+  verbose = c(TRUE, FALSE)
+) {
   verbose <- veupathUtils::matchArg(verbose)
 
   object@links <- pruneCorrelationLinks(