get_region_summary {methrix} | R Documentation |
Extract and summarize methylation or coverage info by regions of interest
get_region_summary( m, regions = NULL, type = "M", how = "mean", overlap_type = "within", na_rm = TRUE, verbose = TRUE )
m |
|
regions |
genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a |
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 |
na_rm |
Remove NA's? Default |
verbose |
Default TRUE |
Takes methrix
object and summarizes regions
a coverage or methylation matrix
data('methrix_data') get_region_summary(m = methrix_data, regions = data.table(chr = 'chr21', start = 27867971, end = 27868103), type = 'M', how = 'mean')