expressionComp: Compare expression estimates between two methods

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

Description

This function allows one to easily compare the expression estimates generated by two different algorithms. Feature / sample combinations that differ above a given threshold can be easily highlighted.

Usage

expressionComp(object1, qcThreshold1, 
                           object2, qcThreshold2, 
                           label1=NULL, label2=NULL,
                           diffThreshold=2,
                           plotType=c("scatterplot","MAplot"))

Arguments

object1	a list containing two elements: ct (the expression estimates) and qc (quality scores)
qcThreshold1	a numeric threshold corresponding to object1$qc below which values are considered low quality.
object2	a list containing two elements: ct (the expression estimates) and qc (quality scores)
qcThreshold2	a numeric threshold corresponding to object2$qc below which values are considered low quality.
label1	an optional label for plotting on the x-axis
label2	an optional label for plotting on the y-axis
diffThreshold	feature / sample combinations for which the expression estimates differ by more than this value are returned by the function and highlighted in the plot.
plotType	scatterplot or MA-plot

Value

This function plots the expresison estimates produced by two different methods. Feature / sample combinations for which the expression estimates differ by more than diffThreshold are returned by the function and highlighted in the plot.

Author(s)

Matthew N. McCall

Examples

  data(lifetech)
  data(qpcRdefault)
  tmp <- expressionComp(object1=lifetech, qcThreshold1=1.25, 
  object2=qpcRdefault,qcThreshold2=0.99,plotType="scatter")

mccallm/miRcomp-shiny documentation built on May 29, 2019, 4:41 a.m.