rnaseqcomp (version 1.0.0)

plotMAD: Plots of Median Absolute Deviation

Description

For each pipeline, two quantification replicates are compared and log scale absolute deviations of signals are calculated. Then, loess smooth on absolute deviation are plotted stratified by detrended log signals.

Usage

plotMAD(dat, type = "l", lwd = 2, col = NULL, lty = 1, xlim = NULL, ylim = NULL, cex.leg = 0.6, xlab = "Detrended logSignal", ylab = "MAD", ...)

Arguments

dat

A rnaseqcomp S4 class object.

type

Plot types (default: 'l').

lwd

Plot line weights (default: 2).

col

Plot colors (default: NULL, colors are assigned by package RColorBrewer).

lty

Plot line styles (default: 1).

xlim

Plot limits of x-axis (default: NULL, limits are estimated automatically).

ylim

Plot limits of y-axis (default: NULL, limits are estimated automatically).

cex.leg

Legend size (default: 0.6).

xlab

Plot label of x-axis (default: 'Detrended logSignal').

ylab

Plot label of y-axis (default: 'MAD').

...

Other parameters for base function plot.

Value

MAD plot

MAD plots for all the quantification pipelines.

MAD

A numeric vector of median absolute deviations.

Examples

data(encodeCells)
evaluationFeature <- encodeCells$genemeta$type == "protein_coding"
calibrationFeature <- encodeCells$genemeta$housekeeping
unitReference <- grepl("Cufflinks",encodeCells$repInfo)
dat <- matrixFilter(encodeCells$gm12878,encodeCells$repInfo,
    evaluationFeature,calibrationFeature,unitReference)
plotMAD(dat)