ApiGetDMCs: Get TOPK=500 DMCs and non-DMCs using moderated-t test

In BPM: Bayesian Purity Model to Estimate Tumor Purity

Description

Get TOPK=500 DMCs and non-DMCs using moderated-t test

Usage

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

Arguments

betaValue	A matrix from TCGA array data
TOPK	An integer number, default 500. Number of DMCs/non-DMCs.
tumorNum	A postive number, First tumorNum columns in betaValue are tumor samples. If tumorNum is NULL, first half of columns are considered as tumor samples,
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. return DMCs (TOPK DMCs and TOPK non-DMCs row index in betaValue)

Note

User can provide the good probes indexes (row number) to filter the probes. A global variable goodProbes are used in this function. goodProbes: probes with SNPs at the CpG or single base extension sites, and corss-reative probes are removed. More details see the reference paper.

BPM documentation built on May 1, 2019, 8:01 p.m.