inHeatmap: Heatmap that represent the fold changes of all the five...

Description Usage Arguments Value Examples

Description

A method to see as an heatmap the logRatios of synthesis, degradation and processing rates and pre-RNA and total RNA concentration of a population of genes, either at the level of etimated or modeled rates.

Usage

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inHeatmap(
  object,
  type = "pre-model",
  breaks = seq(-1, 1, length.out = 51),
  palette = colorRampPalette(c("green", "black", "firebrick3")),
  plot_matureRNA = FALSE,
  absoluteExpression = TRUE,
  show_rowLabels = TRUE,
  clustering = TRUE,
  clustIdx = 3:5
)

## S4 method for signature 'INSPEcT'
inHeatmap(
  object,
  type = "pre-model",
  breaks = seq(-1, 1, length.out = 51),
  palette = colorRampPalette(c("green", "black", "firebrick3")),
  plot_matureRNA = FALSE,
  absoluteExpression = TRUE,
  show_rowLabels = TRUE,
  clustering = TRUE,
  clustIdx = 3:5
)

Arguments

object

An object of class INSPEcT

type

Eiher "pre-model" or "model" to switch between pre-modeled or modeled features

breaks

A vector of breaks for the heatmap

palette

A color generating function, output of colorRampPalette

plot_matureRNA

A logical. If set to TRUE, matrue-RNA is displayed instead of total-RNA (default: FALSE)

absoluteExpression

A logical. If set to FALSE, the plot representing the intensity of expression is omitted. (default=TRUE)

show_rowLabels

A logical defining whether rownames are reported or not. (default=TRUE)

clustering

A logical. If set to FALSE, it displys genes the order they are, with no clustering (default: TRUE)

clustIdx

A numeric. Indicates which of the features are used for the clustering. 0=absoluteExpression; 1=total-RNA/mature-RNA; 2=preMRNA; 3=synthesis; 4=degradation; 5=processing (default=3:5, meaning that synthesis, degradation and processing are used for the clustering)

Value

A list of matrices containing the logRatios for total RNA levels, pre-RNA levels, synthesis rates, degradation rates and processing rates. Matrices are ordered according to the clustering.

Examples

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nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
inHeatmap(nascentInspObj10, 'pre-model')
inHeatmap(nascentInspObj10, 'model')

INSPEcT documentation built on April 29, 2020, 5:19 a.m.