covRNA.R
In covRNA: Multivariate Analysis of Transcriptomic Data

## ---- eval=FALSE, prompt=FALSE------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("covRNA")

## ---- eval=TRUE, message=FALSE, warning=FALSE, prompt=FALSE-------------------
library(covRNA)
data(Baca)

## -----------------------------------------------------------------------------
statBaca <- stat(ExprSet = Baca, npermut = 999, padjust = "BH", nrcor = 2, exprvar = 1)
# or
statBaca <- stat(L = exprs(Baca), R = fData(Baca), Q = pData(Baca), npermut = 999, 
                 padjust = "BH", nrcor = 2, exprvar = 1)

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

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

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

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

## -----------------------------------------------------------------------------
vis(Stat = statBaca, Ord = ordBaca, rangex=1.5, rangey=1.5)

## ---- eval=FALSE, prompt=TRUE-------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("biomaRt")
#  library(biomaRt)

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