plot_rle_boxplot: Boxplot of the relative log expression (RLE) values across...

In MassDynamics/MassExpression: MassExpression

Boxplot of the relative log expression (RLE) values across samples

Description

RLE values are computed using the data from the CompleteIntensityExperiment which contains the intensity values used for the DE analysis (log-transformed, normalised when required).

Usage

plot_rle_boxplot(
  IntensityExperiment,
  CompleteIntensityExperiment,
  includeImputed = FALSE,
  plotRawRLE = FALSE,
  title = "RLE plot",
  format = "html"
)

Arguments

IntensityExperiment	SummarizedExperiment object of the raw data, i.e. including missing values
CompleteIntensityExperiment	SummarizedExperiment object of the data used for the DE analysis (log-transformed, normalised when required).
includeImputed	logical. Whether imputed values should be considered when computing the RLE values.
plotRawRLE	logical. If TRUE RLE using the raw log2 initial data is used. Otherwise, normalised data are used.
title	str. Plot title
format	str. 'pdf' or 'html'

MassDynamics/MassExpression documentation built on May 7, 2023, 11:29 a.m.