reportDiffExp: Get runDEAnalysis .html report

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Get runDEAnalysis .html report

Description

A function to generate .html Rmarkdown report containing the visualizations of the runDEAnalysis function output

Usage

reportDiffExp(
  inSCE,
  study,
  useReducedDim,
  featureDisplay = NULL,
  output_file = NULL,
  output_dir = NULL
)

Arguments

inSCE	A SingleCellExperiment object containing the output from runDEAnalysis function
study	The specific analysis to visualize, used as analysisName argument when running differential expression.
useReducedDim	Specify an embedding for visualizing the relation ship between the conditions.
featureDisplay	The feature ID type to use for displaying. Should exists as a variable name of rowData. Default NULL use rownames of inSCE.
output_file	name of the generated file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.
output_dir	name of the output directory to save the rendered file. If NULL the file is stored to the current working directory. Default NULL.

Value

Saves the HTML report in the specified output directory.

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.