DESeq additional methods {easyRNASeq} | R Documentation |
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.
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,...)
obj |
An object of class |
cex |
The standard |
cond |
A character string describing the first condition. |
linecol |
Defines the line color. |
log |
A character string passed onto
|
name |
Argument passed to the DESeq
|
xlab |
The standard
|
ylab |
The standard
|
ymin |
A numeric value defining the lower limit for the y axis. |
... |
Additional plotting parameters. |
multivariateConditions
returns a boolean describing
whether the data to analyze is multivariate or not
plotDispLSD
and plotDispersionEstimates
returns nothing
Nicolas Delhomme, Bastian Schiffthaler
## 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)