outputDEG: Create markdown string showing deg results.

In carlmurie/RNASeqUtilities: Helper functions for RNASeq analysis and presentation

Description

Input values for parameters 'deg' and 'graphs' must be named deg and graphs. TODO: explore htmltools:knitr_methods to output datatables instead.

Usage

outputDEG(deg, graphs, doSlides = TRUE, onlySigs = FALSE,
  cutOnPval = TRUE, FDRCut = 0.2, pvalCut = 0.01, header = "##")

Arguments

deg	List of deg results from runDEG. Name of deg element will be used as title
graphs	List of graphs from createDEGGraphs. Name of deg element will be used as title
doSlides	Boolean: If TRUE then output markdown slides else produce standard markdown.
onlySigs	Boolean: if TRUE output only genesets that pass the 'FDRCut' threshold (output message if no significant gene sets) else output all genesets. Default is FALSE.
cutOnPval	Boolean: if TRUE use pvalCut for threshold else use FDRCut
FDRCut	FDR threshold to use to determine significance. Default is 0.2.
pvalCut	P value threshold to use to determine significance. Default is 0.01
header	Character string defining markdown header to ouput for each set of results. This is only used if doSlides=FALSE.

Value

Vector of markdown strings

carlmurie/RNASeqUtilities documentation built on Sept. 1, 2019, 11:54 p.m.