Extracts and summarizes methylation or coverage info by regions of interest

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

Value

table of summary statistic for the given region

Details

Takes scMethrix object and summarizes regions

Examples

data('scMethrix_data')
get_region_summary(scMethrix_data,
   regions = GenomicRanges::GRanges(seqnames = c("chr1","chr2"), ranges = IRanges(1,100000000)),
   assay = 'score', by = 'mean')
#> Generating region summary...
#> Summarizing by average
#> Region summary generating in 0.13s
#>     chr start       end n_overlap_CpGs rid        C1        C2     C3        C4
#> 1: chr1     1 100000000             67   1 0.7333333 0.7428571 0.7300 0.6710526
#> 2: chr2     1 100000000             67   2 0.7027027 0.6527778 0.6125 0.5526316