plot.ROTS {ROTS}R Documentation

Plotting of a ROTS object

Description

Plots the ROTS objects created with the ROTS package.

Usage

  ## S3 method for class 'ROTS'
plot(x, fdr=0.05, type=NULL, labels=FALSE, ...)

Arguments

x

A ROTS object created from differential expression testing run by ROTS.

fdr

Selected cutoff for FDR value.

type

Type of plot to be created. Options are: 'volcano', 'heatmap', 'ma', 'reproducibility', 'pvalue', 'pca'.

labels

Option to print labels for differentially expressed features.

...

Other arguments passed to the plot function.

Details

This function plots the results from a ROTS object using given false discovery rate threshold.

Value

Plots the results from ROTS object.

Author(s)

Fatemeh Seyednasrollah, Tomi Suomi, Laura L. Elo Maintainer: Fatemeh Seyednasrollah <fatsey@utu.fi>

See Also

affySpikeIn

Examples

  ## ROTS-statistic for the Affymetrix spike-in data. 
  rots.out <- ROTS(data = affySpikeIn, groups = c(rep(0,5), rep(1,5)),
      B = 100, K = 500 , seed = 1234)
  ## Plotting of the ROTS results.
  plot(rots.out, type="volcano")

[Package ROTS version 1.8.0 Index]