ExpressionViewer: Create a shiny app to display expression values and/or...

In ccb-hms/expressionviewer: Creates a Shiny App to Display Expression of SummarizedExperiments and SGFeatureCounts

Description

This function takes a SummarizedExperiment object, SGFeatureCounts object, or a list of either of these classes and produces a shiny app with a barplot illustrating expression levels per gene and (in the case of SGFeatureCounts) a heatmap illustrating alternative splicing per sample. The assumptions for each object case are listed below.

Usage

ExpressionViewer(
  experiment = counts,
  metaNames = "label.main",
  printNames = " ",
  paper = " ",
  paperlink = " ",
  apptitle = "Expression Viewer:"
)

Details

Summarized Experiment: The sample information wishing to be displayed as the independent variable is in the colData with the column name inputted into the variable "metaNames". The rownames of the expression matrix are gene names.

SGFeatureCounts Object: The sample information wishing to be displayed as the independent variable is in the colData with the column name inputted into the variable "metaNames". The geneID() of the experiment is complete with the gene annotation style desired (NCBI, HGNC Symbol, etc.).

List of either SummarizedExperiments or SGFEatureCounts: The "metaNames" are consistently named for each element of the list. Any class assumptions are retained when part of a list.

Value

A shiny app displaying the expression (and potential splicing) of the experiment input

ccb-hms/expressionviewer documentation built on Dec. 19, 2021, 1:58 p.m.