Nothing
## ---- 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()
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