replicatesCV: Compute the correlation of variation (CV)

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Computes the correlation of variation as defined in Tseng et al. (see References)

Usage

replicatesCV(header, dataset, PlotTitle, col4val, col4anno, plotDesign, showPlot)

Arguments

header	the header of a dataset file generated with generateDatasetFile
dataset	an R data frame generated with generateDatasetFile
PlotTitle	the plot title
col4val	a character string specifying the column whose values will be used to compute the correlation of variation
col4anno	a character string specifying the name of the dataset column to be used to define the replicate, e.g. "GeneName" or "Internal_GeneID"
plotDesign	1 or 2. 1 will generate one window containing all plots, 2 will generate a series of plots.
showPlot	0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows.

Value

The correlation of variation of an siRNA is defined as the standard deviation of its values divided by their mean.

The function generates a plot of the average intensity against the CV for each experiment. The plot will be saved as a pdf and a png file named after the experiment name specified in the header concatenated with the PlotTitle.

The function returns a list containing:

histoName	the plotname
minOfScreens	the number of the first experiment
numOfScreens	the number of the last experiment

References

G. C. Tseng et al. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res, 29(12): 2549-2557, 2001.

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

replicatesCV(header, dataset, "Correlation of Variation versus Mean Intensity", 
"SigIntensity", "GeneName", 1, 0)

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.