BPM (version 1.0.0)

BayPM: Bayesian Purity Model (BPM) Main functions.

Description

Bayesian Purity Model (BPM) Main functions.

Usage

BayPM(betaValue, TOPK = 500, tumorNum = NULL, filterProbes = FALSE,
  userProbes = NULL)

Arguments

betaValue

A matrix,TCGA methlation array data. Each row: loci, Tumor1,Tumor2,...,Normal1,Nomral2,...

TOPK

A number. Number of DMCs/nonDMCs selected

tumorNum

The number of tumor samples. if NULL, the default number is half of column number of dataset.

filterProbes

Logistic. defalut is FALSE. The code use all probes in betaValue. If TRUE, you can use default good probes provided in our code. you can also provide your good probes in userProbes.

userProbes

A number list. The row numbers in betaValue. These rows are considered as good probes.

Value

tumor purity estimation of tumor samples

Examples

# NOT RUN {
### need to install package "limma"
### source("https://bioconductor.org/biocLite.R");biocLite("limma");
BayPM(simUCEC,20,2);

# }