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