inst/doc/Informeasure.R

In Informeasure: R implementation of Information measures

## ---- 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()