compareReplicates: Compare replicate values

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Plots replicate intensities pairwise for each experiment.

Usage

compareReplicates(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 for the plot
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

For each experiment, plots of pairwise comparisons between replicate intensities are generated and saved as a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle, and the number of the experiment.

The function returns a list containing:

plotName	the plot name
minOfScreens	the number of the first experiment
numOfScreens	the number of the last experiment
maxCombinationNum	the number of replicates to compare

See Also

compareReplicaPlates

Examples

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

compareReplicates(header, dataset, "Comparison of Replicates", "SigIntensity", "GeneName", 1, 0)

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