From 4ce9d4f6740e594cf913a80c510bd7f03f6a8dd1 Mon Sep 17 00:00:00 2001
From: "Juan A. Botia" <juanbot@um.es>
Date: Sat, 4 Jul 2020 08:22:04 +0200
Subject: [PATCH] Fixes in getMM

---
 R/main.R     | 4 ++--
 R/netdb.R    | 2 +-
 man/getMM.Rd | 4 ++++
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/R/main.R b/R/main.R
index f1000dc..3fcd66c 100644
--- a/R/main.R
+++ b/R/main.R
@@ -1775,7 +1775,7 @@ corDistance = function(a,b,signed=TRUE,cor.type="pearson"){
 #' @param keep.grey Use grey genes too
 #' @param alt.gene.index You can pass genes in a different order, use this index order for that
 #'
-#' @returnk Depending on the value of table.format, a data.frame with genes and MM values or a list
+#' @return A data.frame with genes and MM values or a list
 #' with genes as keys and the MMs as values
 #' @export
 #'
@@ -2707,7 +2707,7 @@ bottomUpNetwork = function(tissue="SNIG",
     adjacencies <<- apply(tom.matrix,2,sum)
     names(adjacencies) <<- colnames(tom.matrix)
     mms <<- getMM(net=net,genes=NULL,expr.data.file=expr.data,tissue=tissue,
-                  which.one=which.one,in.cluster=F)
+                  which.one=which.one)
   }else{
     adjacencies = apply(tom.matrix,2,sum)
     names(adjacencies) = colnames(tom.matrix)
diff --git a/R/netdb.R b/R/netdb.R
index 39ba133..11fa84c 100644
--- a/R/netdb.R
+++ b/R/netdb.R
@@ -386,7 +386,7 @@ getModuleMostRelevantGenes = function(tissue="SNIG",
                                       cutoff=-1,
                                       expr.data.file=NULL){
 
-  mm = getMM(which.one=which.one,tissue=tissue,table.format = T,
+  mm = getMM(which.one=which.one,tissue=tissue,
              genes=NULL,
              expr.data.file=expr.data.file)
 
diff --git a/man/getMM.Rd b/man/getMM.Rd
index 05254d7..7ecc7d5 100644
--- a/man/getMM.Rd
+++ b/man/getMM.Rd
@@ -39,6 +39,10 @@ which.one set to "new" for a network which is not in the DDBB.}
 
 \item{alt.gene.index}{You can pass genes in a different order, use this index order for that}
 }
+\value{
+A data.frame with genes and MM values or a list
+with genes as keys and the MMs as values
+}
 \description{
 Title Obtain the Module Membership of genes
 This function works by getting the Pearson correlation between the