get_region_summary: Extract and summarize methylation or coverage info by regions...

In CompEpigen/methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Extract and summarize methylation or coverage info by regions of interest

Description

Extract and summarize methylation or coverage info by regions of interest

Usage

get_region_summary(
  m,
  regions = NULL,
  type = "M",
  how = "mean",
  overlap_type = "within",
  na_rm = TRUE,
  elementMetadata.col = NULL,
  verbose = TRUE,
  n_chunks = 1,
  n_cores = 1
)

Arguments

m	methrix object
regions	genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
type	matrix which needs to be summarized. Coule be ‘M', 'C'. Default ’M'
how	mathematical function by which regions should be summarized. Can be one of the following: mean, sum, max, min. Default 'mean'
overlap_type	defines the type of the overlap of the CpG sites with the target region. Default value is 'within'. For detailed description, see the findOverlaps function of the IRanges package.
na_rm	Remove NA's? Default TRUE
elementMetadata.col	columns in rowData(methrix) which needs to be summarised. Default = NULL.
verbose	Default TRUE
n_chunks	Number of chunks to split the methrix object in case it is very large. Default = 1.
n_cores	Number of parallel instances. n_cores should be less than or equal to n_chunks. If n_chunks is not specified, then n_chunks is initialized to be equal to n_cores. Default = 1.

Details

Takes methrix object and summarizes regions

Value

a coverage or methylation matrix

Examples

data('methrix_data')
get_region_summary(m = methrix_data,
regions = data.table(chr = 'chr21', start = 27867971, end =  27868103),
type = 'M', how = 'mean')

CompEpigen/methrix documentation built on July 24, 2024, 5:49 p.m.