probe2gene: Convert the EPIC methylation array probe-level DNA...

In ibphuangchen/genomicWidgets: Useful SCNA and DNA methylation analysis tools

Description

This function extracts the methylation probes located in the promoter region and CpG islands for each gene and use their methylation levels to summerize the gene-level methylation by mean or median.

Usage

probe2gene(probeMat, nThread = NULL, aggr = "gene", use = "median", ...)

Arguments

probeMat	the probe-level DNA methylation matrix (probe by sample), entries are beta values.
nThread	the number of threads to be used for the calculation. If NULL, no parallel computation will be performed.
aggr	to which level should the probe be aggregated, need to be either 'gene' or 'transcript'. Default is 'gene'.
use	specify how the multiple probe values be converted to the single gene-level value. Need to be either 'mean' or 'median'. Default is 'median'.
...	addtional parameter to makeCluster. If you used a Linux or MacOS, it is proper to add type='FORK'.

Value

the gene-level or transcript-level DNA methylation matrix (gene by sample), entries are beta values.

Examples

hnsccSegfile <- system.file("extdata", "hnscc_GDC_methylation_part.tsv", package = "genomicWidgets")
hnsccMethy <- read.table(file = hnsccSegfile, sep = '\t', row.names = 1, header = TRUE)
probe2gene(probeMat=hnsccMethy) #no parallel computation
probe2gene(probeMat=hnsccMethy, nThread = 4) #parallel computation using 4 cores

ibphuangchen/genomicWidgets documentation built on Aug. 20, 2021, 10:55 a.m.