## ---- eval=FALSE, prompt=TRUE--------------------------------------------
## source("https://bioconductor.org/biocLite.R")
## biocLite("covRNA")

## ------------------------------------------------------------------------
library(covRNA)
data(Baca)

## ------------------------------------------------------------------------
statBaca <- stat(ExprSet = Baca, npermut = 999, padjust = "BH", nrcor = 2, exprvar = 1)

## ---- eval=FALSE---------------------------------------------------------
## ls(statBaca)
## adjp <- statBaca$adj.pvalue; adjp

## ------------------------------------------------------------------------
plot(statBaca, xnames = c('cold','ctrl','etoh','salt'), shiftx = -0.1)

## ------------------------------------------------------------------------
ordBaca <- ord(Baca)

## ------------------------------------------------------------------------
plot(ordBaca, feature = "variance")

## ------------------------------------------------------------------------
vis(Stat = statBaca, Ord = ordBaca, rangex=4, rangey=4)

## ---- eval=FALSE, prompt=TRUE--------------------------------------------
## source("https://bioconductor.org/biocLite.R")
## biocLite("biomaRt")
## library(biomaRt)

## ---- eval=FALSE, prompt=TRUE--------------------------------------------
## ensembl <- useEnsembl(biomart = "ensembl")
## listDatasets(ensembl)
## ensemblhuman <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
## listAttributes(ensemblhuman)