make_dnam_se: Transform DNA methylation array into a summarized Experiment...

In TransBioInfoLab/MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Transform DNA methylation array into a summarized Experiment object

Description

Transform DNA methylation array into a summarized Experiment object

Usage

make_dnam_se(
  dnam,
  genome = c("hg38", "hg19"),
  arrayType = c("450k", "EPIC"),
  betaToM = FALSE,
  verbose = FALSE
)

Arguments

dnam	DNA methylation matrix with beta-values or m-values as data, row as cpgs "cg07946458" or regions ("chr1:232:245") and column as samples
genome	Human genome of reference: hg38 or hg19
arrayType	DNA methylation array type (450k or EPIC)
betaToM	indicates if converting methylation beta values to mvalues
verbose	A logical argument indicating if messages output should be provided.

Value

A summarized Experiment object with DNA methylation probes mapped to genomic regions

Examples

library(dplyr)
dnam <- runif(20, min = 0,max = 1) %>% sort %>%
  matrix(ncol = 1) %>%  t
rownames(dnam) <- c("chr3:203727581-203728580")
colnames(dnam) <- paste0("Samples",1:20)
 se <- make_dnam_se(dnam)

TransBioInfoLab/MethReg documentation built on July 28, 2023, 9:17 p.m.