qualityAssessment: Quality Assessment for MicroRNA Expression Estimates

In mccallm/miRcomp: Tools to assess and compare miRNA expression estimatation methods

Description

This function produces several figures to examine quality scores.

Usage

qualityAssessment(object1, object2=NULL, cloglog1=FALSE, cloglog2=FALSE, 
                  na.rm=FALSE, plotType=c("scatterplot","boxplot"), 
                  label1=NULL, label2=NULL) 

Arguments

object1	a list containing two elements: ct (the expression estiamtes) and qc (quality scores)
object2	an optional second list of the same format as object1, used to compare two methods.
cloglog1	if TRUE, the -log(-log(object1$qc)) is plotted. This is useful to visualize certain quality scores such as R-squared.
cloglog2	if TRUE, the -log(-log(object2$qc)) is plotted. This is useful to visualize certain quality scores such as R-squared.
na.rm	if TRUE, quality scores corresponding to NA expression estimates are removed from analysis. This is only used if plotType=="boxplot".
plotType	type of plot to return. Options are a scatterplot or a boxplot.
label1	optional label corresponding to object 1 to be used in plotting.
label2	optional label corresponding to object 2 to be used in plotting.

Value

The function generates a plot of the desired type.

Author(s)

Matthew N. McCall

Examples

  data(lifetech)
  qualityAssessment(lifetech, plotType="boxplot")

  data(qpcRdefault)
  qualityAssessment(object1=lifetech,object2=qpcRdefault,cloglog2=TRUE)

mccallm/miRcomp documentation built on May 7, 2019, 1:26 p.m.