subset_scMethrix: Subsets an 'scMethrix' object based on 'regions', 'contigs'...

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

Description

Subsets an scMethrix object based on regions, contigs and/or samples.

Usage

subset_scMethrix(
  scm = NULL,
  regions = NULL,
  contigs = NULL,
  samples = NULL,
  by = c("include", "exclude"),
  overlap_type = c("within", "start", "end", "any", "equal"),
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
regions	genomic regions to subset by. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
contigs	string; array of chromosome names to subset by
samples	string; array of sample names to subset by
by	string to decide whether to "include" or "exclude" the given criteria from the subset
overlap_type	string; 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 filters CpGs based on region, contig and/or sample. Can either subset (include) to or filter (exclude) the specified parameters.

Value

An object of class scMethrix

Examples

data('scMethrix_data')

contigs <- c("chr1","chr3")
regions <- GenomicRanges::GRanges(seqnames = "chr1", ranges = IRanges(1,100000000)) 
samples <- c("C1","C2")

#Subset to only samples bed1 and bed3, and chromosome 1
subset_scMethrix(scMethrix_data, samples = samples, contigs = contigs, by = "include")

#Subset to only region "chr1:1-5"
subset_scMethrix(scMethrix_data, regions = regions, by = "include")

#Subset to exclude samples bed1 and bed3, and chromosome 1
subset_scMethrix(scMethrix_data, samples = samples, contigs = contigs, by = "exclude")

#Subset to exclude region "chr1:1-5"
subset_scMethrix(scMethrix_data, regions = regions, by = "exclude")

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