AVplot: A function plotting average intensity versus variance

In JungsooGIM/LPEseq: LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates

Description

A function plotting average intensity versus variance

Usage

AVplot(data, avg = "mean", w.value = 0.1, logged = TRUE)

Arguments

data	expression data matrix
avg	measure for average value across the columns of the data matrix (default "mean")
w.value	parameter for lowess weight value (default 0.1)
logged	logical variable indicating log tranformation (default True)

Details

Average versus variance plot of the data can provide a simple characteristics of the data. The larger variance, the higher variability.

Value

plot	average-variance plot

Author(s)

Jungsoo Gim

References

J. Gim and T. Park, PLoS ONE under revision (http://bibs.snu.ac.kr/software/LPEseq)

Examples

## Generating a replicated simulation dataset
data("NBparameter")
simData <- generateData(n.deg=1000)

## Normalization
normData <- generateData(simData[,-7])

## MA transformation
AVplot(normData[,1:3])

JungsooGIM/LPEseq documentation built on May 16, 2019, 10:04 a.m.