titrationResponse: Assess monotone signal across titration

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

Description

This function determines

Usage

titrationResponse(object1, qcThreshold1, object2=NULL, qcThreshold2=NULL, 
                  commonFeatures=TRUE, label1=NULL, label2=NULL)

Arguments

object1	a list containing two elements: ct (the expression estiamtes) and qc (quality scores)
qcThreshold1	a numeric threshold corresponding to object1$qc below which values are considered low quality.
object2	an optional second list of the same format as object1, used to compare two methods.
qcThreshold2	a numeric threshold corresponding to object2$qc below which values are considered low quality.
commonFeatures	if TRUE and object2 is non-NULL, only high quality non-NA features in common between both objects are used.
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

A table listing the number of features showing a monotone titration response and a figure showing the proportion of features showing a monotone titration response vs the difference in pure sample expression.

Author(s)

Matthew N. McCall

Examples

  data(lifetech)
  titrationResponse(object1=lifetech,qcThreshold1=1.25)
  data(qpcRdefault)
  titrationResponse(object1=lifetech,qcThreshold1=1.25,
           object2=qpcRdefault,qcThreshold2=0.99) 

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