biasExploration {TarSeqQC} | R Documentation

## Plot attribute density and boxplot for each bias source quartile or category.

### 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 gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

### 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
    }

[Package TarSeqQC version 1.14.0 Index]