cqnplot: Plot the systematic effect estimated as part of a CQN...

In cqn: Conditional quantile normalization

Description

This function plots the estimated systematic effect which are removed suring CQN normalization.

Usage

cqnplot(x, n = 1, col = "grey60", ylab = "QR fit", xlab = "", type = "l", lty = 1, ...)

Arguments

x	The result of a call to cqn; an object of class cqn.
n	Which systematic effect is plotted.
col	A vector of colors, as in plot.
ylab	y-label as in plot.
xlab	x-label as in plot.
type	type, as in plot.
lty	line type, as in plot.
...	These arguments are passed to matplot

Value

This function is invoked for its side effect.

Author(s)

Kasper Daniel Hansen

Examples

data(montgomery.subset)
data(sizeFactors.subset)
data(uCovar)
cqn.subset <- cqn(montgomery.subset, lengths = uCovar$length, 
                  x = uCovar$gccontent, sizeFactors = sizeFactors.subset,
                  verbose = TRUE)
cqnplot(cqn.subset, n = 1)

Example output

Loading required package: mclust
Package 'mclust' version 5.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: nor1mix
Loading required package: preprocessCore
Loading required package: splines
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

RQ fit ..........
SQN Using 'sigma' instead 'sig2' (= sigma^2) is preferred now
.

cqn documentation built on Nov. 8, 2020, 5:21 p.m.