Last data update: 2014.03.03

R: Plots the average expression against variability using...
diagnosticsVarPlotsR Documentation

Plots the average expression against variability using different summary statistics.

Description

Plots the average expression against variability using different summary statistics to help decide which statistic would be the best with your dataset.

Usage

diagnosticsVarPlots(dat.mat)

Arguments

dat.mat

a matrix with rows as genes and columns as samples.

Details

This function gives you 3 plots one for SD, one for MAD and one for CV against the mean to help you decide which one would be the best with your dataset. It also returns the correlation between each variability statistics and the mean.

Value

3 scatter plots where average expression is on the X-axis and SD, MAD, and CV are on the Y-axis.

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

diagnosticsVarPlots(bock)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(pathVar)
Loading required package: ggplot2
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pathVar/diagnosticsVarPlots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: diagnosticsVarPlots
> ### Title: Plots the average expression against variability using different
> ###   summary statistics.
> ### Aliases: diagnosticsVarPlots
> ### Keywords: methods
> 
> ### ** Examples
> 
> diagnosticsVarPlots(bock)
Warning messages:
1: Removed 629 rows containing non-finite values (stat_smooth). 
2: Removed 629 rows containing missing values (geom_point). 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>