accuracy: Assess the accuracy of the expression estimates

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

Description

This function assesses the signal detect slope (a measure of accuracy) for each feature.

Usage

accuracy(object1, qcThreshold1, object2=NULL, qcThreshold2=NULL, 
commonFeatures=TRUE, bins=3, label1=NULL, label2=NULL)

Arguments

object1	a list containing two elements: ct (the expression estimates) and qc (quality scores)
qcThreshold1	a numeric threshold corresponding to object1$qc below which values are considered low quality.
object2	an optional second list of the same format as object1, used to compare two methods.
qcThreshold2	a numeric threshold corresponding to object2$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.
bins	the number of bins to divide the data into.
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 plot of signal detect slopes stratified by difference in pure sample expression is produced, and a summary (median and MAD) of the signal detect slopes in each bin is returned.

Author(s)

Matthew N. McCall

Examples

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

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