ideal {ideal} | R Documentation |
ideal makes differential expression analysis interactive, easy and reproducible. This function launches the main application included in the package.
ideal( dds_obj = NULL, res_obj = NULL, annotation_obj = NULL, countmatrix = NULL, expdesign = NULL, gene_signatures = NULL )
dds_obj |
A |
res_obj |
A |
annotation_obj |
A |
countmatrix |
A count matrix, with genes as rows and samples as columns. If not provided, it is possible to upload the data during the execution of the Shiny App |
expdesign |
A |
gene_signatures |
A list of vectors, one for each pathway/signature. This
is for example the output of the |
A Shiny App is launched for interactive data exploration and differential expression analysis
# with simulated data... library(DESeq2) dds <- DESeq2::makeExampleDESeqDataSet(n=100, m=8) cm <- counts(dds) cd <- colData(dds) # with the well known airway package... library(airway) data(airway) airway dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design=~cell+dex) ## Not run: ideal() ideal(dds) ideal(dds_airway) dds_airway <- DESeq2::DESeq(dds_airway) res_airway <- DESeq2::results(dds_airway) ideal(dds_airway, res_airway) ## End(Not run)