bio_fc_heatmap: Fold change and pvalues between groups

View source: R/bio_expcomp.R

bio_fc_heatmapR Documentation

Fold change and pvalues between groups

Description

This function exports a complex heatmap looking at the expression of different modules which can be customised

Usage

bio_fc_heatmap(
  exp,
  var,
  prefix = "",
  stars = FALSE,
  overlay = TRUE,
  logp = FALSE
)

Arguments

exp

Expression Data

var

Vector classing samples by variables

prefix

Prefix to Heatmap titles

stars

whether pvales should be written as numeric or start (default=FALSE)

overlay

pvalues on fold change Heatmap or besidde (default = TRUE)

logp

Whether or not to log the pvalues

...

Other parameters to pass to Complex Heatmap

Value

A list containing the mean expression for each group, the fold change between groups, the pvalues comparing the expression from different groups, a heatmap with mean expression, a heatmap containing the fold change and p-values.

Examples

m.var = metadata.final[metadata.final$Pathotype %in% c("Fibroid", "Lymphoid"), ]
exp = t(rldMatrix[, match(m.var$SampleID..QMUL.or.Genentech., colnames(rldMatrix))])
var = droplevels(m.var$Pathotype)

fc = bio_fold.change(exp, var)
p = bio_p.vals(exp, var)

KatrionaGoldmann/BioOutputs documentation built on May 21, 2022, 1:24 p.m.