DEsummaryPanel: Generate the DE summary panel of the shiny app

In bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Generate the DE summary panel of the shiny app

Description

These are the UI and server components of the Heatmap panel of the shiny app. It is generated by including 'DEsummary' in the panels.default argument of generateShinyApp.

Usage

DEsummaryPanelUI(id, metadata, show = TRUE)

DEsummaryPanelServer(id, expression.matrix, metadata, DEresults, anno)

Arguments

id	the input slot that will be used to access the value
metadata	a data frame containing metadata for the samples contained in the expression.matrix; must contain at minimum two columns: the first column must contain the column names of the expression.matrix, while the last column is assumed to contain the experimental conditions that will be tested for differential expression; a list (of the same length as modality) can be provided if #' length(modality) > 1
show	whether to show the panel or not; default is TRUE; there for compatibility with specifying panels to show
expression.matrix	the expression matrix; rows correspond to genes and columns correspond to samples; usually preprocessed by preprocessExpressionMatrix; a list (of the same length as modality) can be provided if #' length(modality) > 1
DEresults	differential expression results output from DEpanelServer; a reactive list with slots 'DEtable' (all genes), 'DEtableSubset' (only DE genes), 'lfcThreshold' and 'pvalThreshold'
anno	annotation data frame containing a match between the row names of the expression.matrix (usually ENSEMBL IDs) and the gene names that should be rendered within the app and in output files; this object is created by generateShinyApp using the org.db specified

Value

The UI and Server components of the shiny module, that can be used within the UI and Server definitions of a shiny app.

bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.