em.draw: Plot of transformed expression produced by EM algorithm

Description Usage Arguments Value Author(s)

Description

Given a numeric vector, a plot of four panels is drawn: 1) fitted mixture distribution 2) transformed expression against original expression 3) histogram of original expression 4) progression of log-likelihood during the fit

Usage

1
2
  em.draw(vec, cl, threshold=0.0001)
  #em.draw(vec, cl=1-metastasis, threshold=0.0001)

Arguments

vec

A numeric vector, especially a particular row of expression matrix

cl

A vector of 0s and 1s. Use 1 for normal phenotype and 0 for non-normal phenotype. If left blank, all samples will be labeled as normal phenotype. Normal component of mixture is estimated using samples with normal phenotype only. POE for samples with non-normal phenotype will be calculated after EM algorithm finishes ML estimation.

threshold

Crieterion for convergence in likelihood.

Value

A plot of four panels will appear upon the call.

Author(s)

Debashis Ghosh <ghoshd@psu.edu> , Hyungwon Choi <hyung_won_choi@nuhs.edu.sg>


metaArray documentation built on April 29, 2020, 2:12 a.m.