## ---- 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)