DESeq additional methods {easyRNASeq} | R Documentation

## Extension for the DESeq package

### Description

- `multivariateConditions` is simply an accessor for the `multivariateConditions` slot of a `CountDataSet` object

- `plotDispLSD` is a function similar to `plotDispEsts` that adds a density estimate as a colored heatmap from grey (few) to yellow (many).

- `plotDispersionEstimates` offers the functionality to plot the dispersion estimate as described in the DESeq vignette.

### Usage

    multivariateConditions(obj)
    plotDispLSD(obj, name = NULL, ymin,
    linecol = "#00000080", xlab = "mean of normalized counts",
    ylab = "dispersion", log = "xy", cex = 0.45, ...)
    plotDispersionEstimates(obj,cond,log,...)

### Arguments

`obj` | An object of class `CountDataSet`.
`cex` | The standard `plot.default` parameter.
`cond` | A character string describing the first condition.
`linecol` | Defines the line color.
`log` | A character string passed onto `plot.default`.
`name` | Argument passed to the DESeq `fitInfo` function.
`xlab` | The standard `plot.default` parameter.
`ylab` | The standard `plot.default` parameter.
`ymin` | A numeric value defining the lower limit for the y axis.
`...` | Additional plotting parameters.

### Value

- `multivariateConditions` returns a boolean describing whether the data to analyze is multivariate or not

- `plotDispLSD` and `plotDispersionEstimates` returns nothing

### Author(s)

Nicolas Delhomme, Bastian Schiffthaler

### See Also

`CountDataSet` `plotDispEsts`

### Examples

    	## Not run:
    	# these are helper function for the DESeq package
    	# refer to its vignette first
    	cds <- newCountDataSet(countData,conditions)
    	cds <- estimateSizeFactors(cds)
    	cds <- estimateDispersions(cds)
    	mVar <- multivariateConditions(cds)
    	plotDispersionEstimates(cds,conditions[1])

    ## End(Not run)

[Package easyRNASeq version 2.24.1 Index]