rnaseqcomp (version 1.0.0)

plotNE: Plots of Express And Non-express Features

Description

For each pipeline, two quantification replicates are compared and proportions of both-express, both-non-express and either-or-express features are calculated. Then, reverse proportion accumulation for either-or-express features are plotted stratified by detrended log signals.

Usage

plotNE(dat, step = 0.1, type = "l", lwd = 2, col = NULL, lty = 1, xlim = NULL, ylim = NULL, cex.leg = 0.6, xlab = "Detrended logSignal", ylab = "Proportion of discordant calls", ...)

Arguments

dat

A rnaseqcomp S4 class object.

step

Plot steps on x-axis.

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: 'Proportion of discordant calls').

...

Other parameters for base function plot.

Value

Either-or-express plot

Plots for all the quantification pipelines.

matrix

A proportion matrix of express, non-express and either-or-express for all pipelines.

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)
plotNE(dat)