bin_scMethrix: Bins the ranges of an 'scMethrix' object.

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

Description

Bins the ranges of an scMethrix object.

Usage

bin_scMethrix(
  scm = NULL,
  regions = NULL,
  bin_size = 1e+05,
  bin_by = c("bp", "cpg"),
  trans = NULL,
  overlap_type = c("within", "start", "end", "any", "equal"),
  h5_dir = NULL,
  verbose = TRUE,
  batch_size = 20,
  n_threads = 1,
  replace = FALSE
)

Arguments

scm	scMethrix; the single cell methylation experiment
regions	Granges; The regions from which to make the bins.
bin_size	integer; The size of each bin. First bin will begin at the start position of the first genomic region on the chromosome. If NULL, there will be one bin per region. Default 100000.
bin_by	character; can create bins by # of base pairs "bp" or by # of CpG sites "cpg". Default "bp"
trans	named vector of closures; The transforms for each assay in a named vector. Default NULL, meaning that operations for "counts" assay is sum(x, na.rm=TRUE), and for all other assays is mean(x, na.rm=TRUE)
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.
h5_dir	string; The directory to use. Will be created if it does not exist. Default = NULL
verbose	boolean; Flag for outputting function status messages. Default = TRUE
batch_size	integer; The maximum number of elements to process at once.
n_threads	integer; Maximum number of parallel instances. Default = 1
replace	boolean; flag for whether to delete the contents of h5_dir before saving

Details

Uses the inputted function to transform an assay in the scMethrix object. Typically, most assays will use either mean (for measurements) or sum (for counts). The transform is applied column-wise to optimize how HDF5 files access sample data. If HDF5 objects are used, transform functions should be from DelayedMatrixStats.

In the output object, the number of CpGs in each region is saved in mcol(scm)$n_cpgs.

Reduced dimensionality data will be discarded.

Value

An scMethrix object

Examples

data('scMethrix_data')
regions <- GRanges(seqnames = c("chr1"), ranges = IRanges(1,200000000)) 
regions <- unlist(tile(regions,10))
bin_scMethrix(scMethrix_data, regions = regions)

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