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

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

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

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

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

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.