miRcomp (version 1.2.2)

qualityAssessment: Quality Assessment for MicroRNA Expression Estimates

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.

Examples

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

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