Bins the ranges of an scMethrix object.
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 )
| scm |
|
|---|---|
| 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 |
| 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 |
An scMethrix object
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.
data('scMethrix_data') regions <- GRanges(seqnames = c("chr1"), ranges = IRanges(1,200000000)) regions <- unlist(tile(regions,10)) bin_scMethrix(scMethrix_data, regions = regions)#>#>#>#>#>#>#>#>#>#>#>#>#> An object of class scMethrix #> n_CpGs: 131 #> n_samples: 4 #> assays: score, counts #> reduced dims: #> is_h5: FALSE #> Reference: hg19 #> Physical size: 37.5 Kb