get_region_summary: Extracts and summarizes methylation or coverage info by...

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Extracts and summarizes methylation or coverage info by regions of interest

Usage

get_region_summary(
  scm = NULL,
  assay = "score",
  regions = NULL,
  group = NULL,
  n_chunks = 1,
  n_threads = 1,
  by = c("mean", "median", "maximum", "minimum", "sum", "sd"),
  overlap_type = c("within", "start", "end", "any", "equal"),
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
assay	string; name of an existing assay. Default = "score"
regions	GRanges; genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
group	a column name from sample annotation that defines groups. In this case, the number of min_samples will be tested group-wise.
n_chunks	integer; Number of chunks to split the scMethrix object in case it is very large. Default = 1
n_threads	integer; Maximum number of parallel instances. Default = 1
by	closure; 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.
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Details

Takes scMethrix object and summarizes regions

Value

table of summary statistic for the given region

Examples

data('scMethrix_data')
get_region_summary(scMethrix_data,
   regions = GenomicRanges::GRanges(seqnames = c("chr1","chr2"), ranges = IRanges(1,100000000)),
   assay = 'score', by = 'mean')

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.