diff --git a/RBiomirGS/R/mirnaGS.R b/RBiomirGS/R/mirnaGS.R index 03a69e7..6e5e362 100755 --- 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 index c48b3fa..07f7468 100755 --- a/RBiomirGS/man/rbiomirgs_logistic.Rd +++ b/RBiomirGS/man/rbiomirgs_logistic.Rd @@ -6,7 +6,7 @@ \usage{ rbiomirgs_logistic(objTitle = "mirna_mrna", mirnascoreTitle = "mirnascore", mrnascoreTitle = "mrnascore", defile = NULL, mirna_DE = NULL, - var_mirnaName = "miRNA", var_mirnaFC = "logFC", logFC = TRUE, + var_mirnaName = "miRNA", var_mirnaFC = "logFC", ratioFC = FALSE, var_mirnaP = "p.value", mrnalist = NULL, mrna_Weight = NULL, gs_file = NULL, optim_method = "IWLS", p.adj = "fdr", ..., parallelComputing = FALSE, clusterType = "PSOCK") @@ -26,7 +26,7 @@ rbiomirgs_logistic(objTitle = "mirna_mrna", mirnascoreTitle = "mirnascore", \item{var_mirnaFC}{Variable name for miRNA fold change (or log transformed FC) in the DE list. Default is \code{"logFC"}.} -\item{logFC}{Wether logFC (i.e. log2(FC)) is used for the fold change variable. Default is \code{TRUE}.} +\item{ratioFC}{Wether the FC provided is a ratio value. Default is \code{FALSE}.} \item{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.} diff --git a/README.md b/README.md index 42d7b60..304de20 100755 --- 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