plotRatioDensity: plotRatioDensity Function to plot density of ratios between...

Description Usage Arguments Details Value Author(s) References Examples

Description

This function plots the expression of the supplied object, using ratios between a pair of selected treatments.

Usage

1
2
plotRatioDensity(se, groupings= NULL, treatment1=NULL,
treatment2=NULL, mode_mean=TRUE, LOG2=TRUE,...)

Arguments

se

A SummarizedExperiment object.

groupings

A grouping (annotation); groupings="annotation.ZA"

treatment1

Symbol, treatment 1.

treatment2

Symbol, treatment 2.

mode_mean

Boolean, Calculate RowMeans or RowMedians.

LOG2

Boolean, Calculate LOG2.

...

Passthrough arguments to boxplot (additional arguments affecting the summary produced).

Details

This function plots expression of the supplied object using ratios of treatment1/treatment2.

Value

Returns an invisible data frame containing the x-values and corresponding density for each applicable annotation column entry.

Author(s)

AJ Vaestermark, JR Walters.

References

The "doseR" package, 2018 (in press).

Examples

1
2
3
data(hmel.se)
plotRatioDensity(se, groupings='annotation.ZA', treatment1 = 'Male',
treatment2 = 'Female',lty=1,type="l")

avastermark19/doseR_0.99.15 documentation built on May 23, 2019, 3:04 a.m.