geneselect: The server function of the geneselect module

In pinin4fjords/shinyngs: Shiny apps for NGS data

The server function of the geneselect module

Description

This module provides controls for selecting genes (matrix rows) by various criteria such as variance and gene set.

Usage

geneselect(
  input,
  output,
  session,
  eselist,
  getExperiment,
  var_n = 50,
  var_max = 500,
  selectSamples = reactive({
     colnames(getExperiment())
 }),
  getAssay,
  provide_all = TRUE,
  provide_none = FALSE,
  default = NULL
)

Arguments

input	Input object
output	Output object
session	Session object
eselist	ExploratorySummarizedExperimentList object containing ExploratorySummarizedExperiment objects
getExperiment	Reactive expression which returns a ExploratorySummarizedExperiment object with assay and experimental data
var_n	The number of rows to select when doing so by variance. Default = 50
var_max	The maximum umber of rows to select when doing so by variance. Default = 500
selectSamples	A reactive expression that provides a vector of samples to use, e.g. in row-wise variance calculation
getAssay	A reactive expression providing the current assay selection.
provide_all	Allow the 'all rows' selection in the UI? Means we don't have to calculate variance so the display is quicker, but it's a bad idea for e.g. heatmaps where the visual scales by the number of rows.
provide_none	Allow the 'none' selection in the UI to make row selection optional.
default	Default gene selection method

Value

output A list of reactive functions for interrogating the selected rows.

Examples

geneselect_functions <- callModule(geneselect, "heatmap", getExperiments)

pinin4fjords/shinyngs documentation built on Feb. 28, 2024, 10:19 a.m.