Compare replicate values

Description

Plots replicate intensities pairwise for each experiment.

Usage

1
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

1
2
3
4
data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

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

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.