easyRNASeq (version 2.8.2)

DESeq additional methods: Extension for the DESeq package

Description

• multivariateConditionsis simply an accessor for themultivariateConditionsslot of aCountDataSetobject

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

• • multivariateConditionsreturns a boolean describing whether the data to analyze is multivariate or not
• plotDispLSD and plotDispersionEstimates
• returns nothing

See Also

CountDataSet plotDispEsts

Examples

# 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])