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