getCpGs: Get CpG (and non-CpG) loci from a single sample BSseq object.

In hansenlab/bsseq: Analyze, manage and store whole-genome methylation data

Get CpG (and non-CpG) loci from a single sample BSseq object.

Description

This function identifies CpG (and non-CpG) loci from a single sample BSseq object using scaled likelihoods computed from the count of CpG sites and Non-CpG sites mapped to the loci, based on the specified type, and minimum scaled likelihood (threshold). The function only work for BSseq objects generated using read.bedMethyl.

Usage

getCpGs(BSseq, type = c("homozygous", "heterozygous", "allCpG", "nonCpG"), threshold = 0.99, e = NULL)

Arguments

BSseq	An single sample object of class BSseq.
type	A character string specifying the type of loci to extract. Must be one of "homozygous", "heterozygous", "allCpG", or "nonCpG".
threshold	A numeric value between 0 and 1 specifying the minimum likelihood threshold required for loci to be included.
e	An optional numeric value representing the error rate. If NULL, the error rate is estimated using estimateErrorRate.

Value

An integer vector of indices representing the loci that match the criteria.

Author(s)

Søren Blikdal Hansen ([e-mail])

See Also

BSseq for the BSseq class, read.bedMethyl for details on reading data into a BSseq object, estimateErrorRate for estimating the CpG-specific error rate.

Examples

# Example input files
infiles <- c(system.file("extdata/HG002_nanopore_test.bedMethyl.gz",
                         package = "bsseq"),
             system.file("extdata/HG002_pacbio_test.bedMethyl.gz",
                         package = "bsseq"))

# Run the function to import data
bsseq <- read.bedMethyl(files = infiles,
                        colData = DataFrame(row.names = c("test_nanopore", 
                                                          "test_pacbio")),
                        strandCollapse = TRUE,
                        verbose = TRUE)

# Filter CpG sites for the Nanopore dataset
bsseq_nano <- bsseq[, 1]
bsseq_nano_99All_filtered <- bsseq[getCpGs(bsseq_nano, 
                                           type = "allCpG", threshold = 0.99)]

# Filter CpG sites for the PacBio dataset
bsseq_pacbio <- bsseq[, 2]
bsseq_pacbio_99All_filtered <- bsseq[getCpGs(bsseq_pacbio, 
                                             type = "allCpG", threshold = 0.99)]

hansenlab/bsseq documentation built on June 12, 2025, 7:42 p.m.