## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "##>" ) ## ---- echo = FALSE, results = 'hide', warning = FALSE------------------------- suppressPackageStartupMessages(library(SummarizedExperiment)) ## ----------------------------------------------------------------------------- library(Informeasure) library(SummarizedExperiment) load(system.file("extdata/tcga.brca.testdata.Rdata", package="Informeasure")) mRNAexpression <- as.matrix(mRNAexpression) se.mRNAexpression = SummarizedExperiment(assays = list(mRNAexpression = mRNAexpression)) assays(se.mRNAexpression)[["log2"]] <- log2(assays(se.mRNAexpression)[["mRNAexpression"]]+1) x <- assays(se.mRNAexpression["BRCA1", ])$log2 y <- assays(se.mRNAexpression["BARD1", ])$log2 XY <- discretize2D(x,y) MI.measure(XY) ## ----------------------------------------------------------------------------- library(Informeasure) library(SummarizedExperiment) load(system.file("extdata/tcga.brca.testdata.Rdata", package="Informeasure")) lncRNAexpression <- as.matrix(lncRNAexpression) se.lncRNAexpression = SummarizedExperiment(assays = list(lncRNAexpression = lncRNAexpression)) miRNAexpression <- as.matrix(miRNAexpression) se.miRNAexpression = SummarizedExperiment(assays = list(miRNAexpression = miRNAexpression)) mRNAexpression <- as.matrix(mRNAexpression) se.mRNAexpression = SummarizedExperiment(assays = list(mRNAexpression = mRNAexpression)) assays(se.lncRNAexpression)[["log2"]] <- log2(assays(se.lncRNAexpression)[["lncRNAexpression"]] + 1) assays(se.miRNAexpression)[["log2"]] <- log2(assays(se.miRNAexpression)[["miRNAexpression"]] + 1) assays(se.mRNAexpression)[["log2"]] <- log2(assays(se.mRNAexpression)[["mRNAexpression"]] + 1) x <- assays(se.miRNAexpression["hsa-miR-26a-5p", ])$log2 y <- assays(se.mRNAexpression["PTEN", ])$log2 z <- assays(se.lncRNAexpression["PTENP1", ])$log2 XYZ <- discretize3D(x,y,z) CMI.measure(XYZ) ## ----------------------------------------------------------------------------- library(Informeasure) library(SummarizedExperiment) load(system.file("extdata/tcga.brca.testdata.Rdata", package="Informeasure")) miRNAexpression <- as.matrix(miRNAexpression) se.miRNAexpression = SummarizedExperiment(assays = list(miRNAexpression = miRNAexpression)) mRNAexpression <- as.matrix(mRNAexpression) se.mRNAexpression = SummarizedExperiment(assays = list(mRNAexpression = mRNAexpression)) assays(se.miRNAexpression)[["log2"]] <- log2(assays(se.miRNAexpression)[["miRNAexpression"]] + 1) assays(se.mRNAexpression)[["log2"]] <- log2(assays(se.mRNAexpression)[["mRNAexpression"]] + 1) x <- assays(se.miRNAexpression["hsa-miR-34a-5p", ])$log2 y <- assays(se.mRNAexpression["MYC", ])$log2 z <- assays(se.miRNAexpression["hsa-miR-34b-5p", ])$log2 XYZ <- discretize3D(x,y,z) II.measure(XYZ) ## ----------------------------------------------------------------------------- library(Informeasure) library(SummarizedExperiment) load(system.file("extdata/tcga.brca.testdata.Rdata", package="Informeasure")) miRNAexpression <- as.matrix(miRNAexpression) se.miRNAexpression = SummarizedExperiment(assays = list(miRNAexpression = miRNAexpression)) mRNAexpression <- as.matrix(mRNAexpression) se.mRNAexpression = SummarizedExperiment(assays = list(mRNAexpression = mRNAexpression)) assays(se.miRNAexpression)[["log2"]] <- log2(assays(se.miRNAexpression)[["miRNAexpression"]] + 1) assays(se.mRNAexpression)[["log2"]] <- log2(assays(se.mRNAexpression)[["mRNAexpression"]] + 1) x <- assays(se.miRNAexpression["hsa-miR-34a-5p", ])$log2 y <- assays(se.miRNAexpression["hsa-miR-34b-5p", ])$log2 z <- assays(se.mRNAexpression["MYC", ])$log2 XYZ <- discretize3D(x,y,z) PID.measure(XYZ) ## ----------------------------------------------------------------------------- library(Informeasure) library(SummarizedExperiment) load(system.file("extdata/tcga.brca.testdata.Rdata", package="Informeasure")) lncRNAexpression <- as.matrix(lncRNAexpression) se.lncRNAexpression = SummarizedExperiment(assays = list(lncRNAexpression = lncRNAexpression)) miRNAexpression <- as.matrix(miRNAexpression) se.miRNAexpression = SummarizedExperiment(assays = list(miRNAexpression = miRNAexpression)) mRNAexpression <- as.matrix(mRNAexpression) se.mRNAexpression = SummarizedExperiment(assays = list(mRNAexpression = mRNAexpression)) assays(se.lncRNAexpression)[["log2"]] <- log2(assays(se.lncRNAexpression)[["lncRNAexpression"]] + 1) assays(se.miRNAexpression)[["log2"]] <- log2(assays(se.miRNAexpression)[["miRNAexpression"]] + 1) assays(se.mRNAexpression)[["log2"]] <- log2(assays(se.mRNAexpression)[["mRNAexpression"]] + 1) x <- assays(se.miRNAexpression["hsa-miR-26a-5p", ])$log2 y <- assays(se.mRNAexpression["PTEN", ])$log2 z <- assays(se.lncRNAexpression["PTENP1", ])$log2 XYZ <- discretize3D(x,y,z) PMI.measure(XYZ) ## ----------------------------------------------------------------------------- sessionInfo()