0.2.9

jzhangc · Feb 22, 2018 · d40f48d · d40f48d
1 parent 604ba41
commit d40f48d
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/RBiomirGS/R/mirnaGS.R b/RBiomirGS/R/mirnaGS.R
@@ -41,7 +41,7 @@ rbiomirgs_gmt <- function(file){
 #' @param mirna_DE DE list of miRNAs of interest. This can be a \code{data.frame}, \code{matrix} or \code{list} object.
 #' @param var_mirnaName Variable name for miRNA names in the DE list. Default is \code{"miRNA"}.
 #' @param var_mirnaFC Variable name for miRNA fold change (or log transformed FC) in the DE list. Default is \code{"logFC"}.
-#' @param logFC Wether logFC (i.e. log2(FC)) is used for the fold change variable. Default is \code{TRUE}.
+#' @param ratioFC Wether the FC provided is a ratio value. Default is \code{FALSE}.
 #' @param var_mirnaP Variable name for miRNA p value in the DE list. Default is \code{"p.value"}. Note that the value will be -log10 transformed before calculating the miRNA score.
 #' @param mrnalist List containing the mRNA targets for the miRNAs of interest. This is a \code{list} object and can be obtained from \code{\link{rbiomirgs_mrnascan}} function.
 #' @param mrna_Weight A vector weight for the miRNA-mRNA interaction. Default is \code{NULL}.
@@ -70,7 +70,7 @@ rbiomirgs_logistic <- function(objTitle = "mirna_mrna",
                                mirnascoreTitle = "mirnascore",
                                mrnascoreTitle = "mrnascore",
                                defile = NULL,
-                               mirna_DE = NULL, var_mirnaName = "miRNA", var_mirnaFC = "logFC", logFC = TRUE,
+                               mirna_DE = NULL, var_mirnaName = "miRNA", var_mirnaFC = "logFC", ratioFC = FALSE,
                                var_mirnaP = "p.value",
                                mrnalist = NULL, mrna_Weight = NULL,
                                gs_file = NULL,
@@ -92,26 +92,26 @@ rbiomirgs_logistic <- function(objTitle = "mirna_mrna",
   if (is.null(defile)){
     if (class(mirna_DE) == "data.frame"){
       mirna.DE <- mirna_DE
-      if (logFC){
-        mirna.score <- sign(mirna.DE[, var_mirnaFC]) * (-log10(mirna.DE[, var_mirnaP]))
-      } else {
+      if (ratioFC){
         mirna.score <- sign(log2(mirna.DE[, var_mirnaFC])) * (-log10(mirna.DE[, var_mirnaP]))
+      } else {
+        mirna.score <- sign(mirna.DE[, var_mirnaFC]) * (-log10(mirna.DE[, var_mirnaP]))
       }
       names(mirna.score) <- mirna.DE[, var_mirnaName]
     } else if (class(mirna_DE == "matrix")){
       mirna.DE <- mirna_DE
-      if (logFC){
-        mirna.score <- sign(as.numeric(mirna.DE[, var_mirnaFC])) * (-log10(as.numeric(mirna.DE[, var_mirnaP])))
-      } else {
+      if (ratioFC){
         mirna.score <- sign(log2(as.numeric(mirna.DE[, var_mirnaFC]))) * (-log10(as.numeric(mirna.DE[, var_mirnaP])))
+      } else {
+        mirna.score <- sign(as.numeric(mirna.DE[, var_mirnaFC])) * (-log10(as.numeric(mirna.DE[, var_mirnaP])))
       }
       names(mirna.score) <- mirna.DE[, var_mirnaName]
     } else if (class(mirna_DE) == "list"){
       mirna.DE <- mirna_DE
-      if (logFC){
-        mirna.score <- sign(mirna.DE[[var_mirnaFC]]) * (-log10(mirna.DE[[var_mirnaP]]))
-      } else {
+      if (ratioFC){
         mirna.score <- sign(log2(mirna.DE[[var_mirnaFC]])) * (-log10(mirna.DE[[var_mirnaP]]))
+      } else {
+        mirna.score <- sign(mirna.DE[[var_mirnaFC]]) * (-log10(mirna.DE[[var_mirnaP]]))
       }
       names(mirna.score) <- mirna.DE[[var_mirnaName]]
     } else {

diff --git a/RBiomirGS/man/rbiomirgs_logistic.Rd b/RBiomirGS/man/rbiomirgs_logistic.Rd
diff --git a/README.md b/README.md
@@ -31,7 +31,7 @@ Installation:
 Update log
 
     0.2.9 (Feb.22.2018)
-      - logFC arugment added to rbiomirgs_logistic()
+      - ratioFC arugment added to rbiomirgs_logistic()
       - The default value for var_mirnaFC of rbiomirgs_logistic() changed to "logFC"
 
     0.2.7 - 0.2.8