indexregionfunc {IMA}R Documentation

Region-level Methylation Index Calculation

Description

For each specific region of a gene, IMA will collect the loci within it and derive an index of overall region methylation value. Currently, there are three different index metrics implemented in IMA: mean, median, and Tukey's Biweight robust average. By default, the mean beta values will be used as the region's methylation index for further analysis.

Usage

indexregionfunc(indexlist, beta, indexmethod = c("mean", "median", "tbrm"))

Arguments

indexlist

specify the region(s) of interest

beta

β value matrix for the 450K microarray

indexmethod

The methods available to derive an index of overall region methylation value for each region. The options are mean, median, and Tukey's Biweight robust average.

Value

return a matrix of the index of overall methylation value for the region(s) of interest

Author(s)

Dan Wang; Li Yan; Qiang Hu;Dominic J Smiraglia; Song Liu

Maintainer: Dan Wang <wangdan412@gmail.com>

Examples

# >beta = dataf@bmatrix;##dataf is returned by IMA.methy450PP() function
# >betar =indexregionfunc(indexlist=dataf@TSS1500Ind,beta=beta,indexmethod="mean")

[Package IMA version 3.1.2 Index]