pcaExplorer {pcaExplorer} | R Documentation |
Launch a Shiny App for interactive exploration of a dataset from the perspective of Principal Components Analysis
pcaExplorer( dds = NULL, dst = NULL, countmatrix = NULL, coldata = NULL, pca2go = NULL, annotation = NULL, runLocal = TRUE )
dds |
A |
dst |
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 |
coldata |
A data.frame containing the info on the covariates of each sample. If not provided, it is possible to upload the data during the execution of the Shiny App |
pca2go |
An object generated by the |
annotation |
A |
runLocal |
A logical indicating whether the app is to be run locally or remotely on a server, which determines how documentation will be accessed. |
A Shiny App is launched for interactive data exploration
library(airway) data(airway) airway dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design = ~dex+cell) ## Not run: rld_airway <- DESeq2::rlogTransformation(dds_airway) pcaExplorer(dds_airway, rld_airway) pcaExplorer(countmatrix = counts(dds_airway), coldata = colData(dds_airway)) pcaExplorer() # and then upload count matrix, covariate matrix (and eventual annotation) ## End(Not run)