TargetExperiment-biasExploration: Plot attribute density and boxplot for each bias source...

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

biasExploration plots density and box-plot of the analyzed attribute for each bias source' quartiles per categories. It helps the identification of some bias due to high source values, for example, high gc content. This graphics could plot together using the ggplot2 geom_violin method.

Usage

biasExploration(object, source = c("length", "gc", "pool"), dens = FALSE)

## S4 method for signature 'TargetExperiment'
biasExploration(object, source = c("length",
    "gc", "pool"), dens = FALSE)

Arguments

object	TargetExperiment class object.
source	Character 'gc','length', or 'pool' indicating the source bias. In the case of 'gc' and 'length', it will be categorized in four groups according to its quartiles. In the case of 'pool', its groups will be conserved.
dens	Logical indicating if density plot should be added using the geom_violin ggplot2 method.

Value

ggplot2 graphics.

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

See Also

plot, plotFeatPerform

Examples

## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")

# Attribute boxplot and density plot exploration
g<-biasExploration(ampliPanel,source="gc", dens=TRUE)
# x11(type="cairo")
if(interactive()){
g
}

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.