plotPWF {goseq} | R Documentation

## Plot the Probability Weighting Function

### Description

Plots the Probability Weighting Function created by `nullp` by binning together genes.

### Usage

    plotPWF(pwf,binsize="auto",pwf_col=3,pwf_lwd=2,xlab="Biased Data in <binsize> gene bins.",ylab="Proportion DE",...)

### Arguments

`pwf` | A data frame with 3 columns named DEgenes, bias.data & pwf and row names giving the gene names. Usually generated by `nullp`.
`binsize` | Calculate and plot the fraction of genes that are DE in bins of this size. If set to "auto" the best binsize for visualization is attempted to be found automatically.
`pwf_col` | The colour of the probability weighting function
`pwf_lwd` | The width of the probability weighting function
`xlab` | The x-axis label. `<binsize>` is replaced by the binsize used.
`ylab` | The y-axis label.
`...` | Extra arguments that are passed to plot.

### Details

This function is almost always called using the output from the `nullp` function. However, it can be used to visualize the length (or any other type of quantifyable) bias in ability to detect DE in a data set. The `pwf` arguement needs to be a data frame with 3 columns each containing numeric entries (although NAs are permitted in the bias.data and pwf columns), which must be named "DEgenes", "bias.data" and "pwf", although they can appear in any order. The row names are taken to be the gene names. The DEgenes column should be 0s or 1s where 1 represents a DE gene, 0 a gene which is not DE. The bias.data column is a quantification of the quantity for which there is a bias in detecting DE for the associated gene, this is usually gene length or the number of counts associated with a gene. Finally, the pwf column gives the probability weighting to be applied for a given gene.

### Value

Nothing is returned.

### Author(s)

Matthew D. Young myoung@wehi.edu.au

### References

Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A. (2010) Gene ontology analysis for RNA-seq: accounting for selection bias Genome Biology Date: Feb 2010 Vol: 11 Issue: 2 Pages: R14

### See Also

`nullp`

### Examples

    data(genes)
    pwf <- nullp(genes, 'hg19', 'ensGene',plot.fit=FALSE)
    plotPWF(pwf,binsize=200)

[Package goseq version 1.42.0 Index]