read.modkit: Construct BSseq objects from nanopore BED files

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

Construct BSseq objects from nanopore BED files

Description

Construct BSseq objects from nanopore BED files

Usage

read.modkit(
    files,
    colData = NULL,
    rmZeroCov = FALSE,
    strandCollapse = TRUE
)

Arguments

files	vector, BED files
colData	data frame, phenotypic data with samples as rows and variables as columns
rmZeroCov	A logical (1) indicating whether methylation loci that have zero coverage in all samples be removed
strandCollapse	A logical (1) indicating whether stand-symmetric methylation loci (i.e. CpGs) should be collapsed across strands

Details

This function reads in nanopore sequencing modified BED files to Bsseq objects. Nanopore sequencing data (i.e. aggregated modified base counts) is stored in modified-base BAM files. These modified-base BAM files are converted to bedMethyl (BED) files using modkit.

Details for modkit

Modkit outputs modified reads, unmodified reads, ambiguous modification reads (reads where the probability was below the threshold and usually failing the lowest 10th percentile), and other modified reads.

modkit to Bsseq object

After creating BED files using modkit, the BED files are read in and the Bsseq object is constructed via read.modkit() function. The function reads in BED files, extract genomic regions, methylation, coverage, ambiguous modification status data and sample information and then construct Bsseq object using BSseq function within the package. Other modification bases such as hydroxymethylation are extracted and added to the methylation matrix when present.

Value

BSseq objects

Examples

# No other modification present
files <- c(system.file("extdata/modkit/chr21.chr22.HG002.top1000.bed.gz", package = "bsseq"))
bsseq_nano <- read.modkit(files, rmZeroCov = FALSE, strandCollapse=FALSE)

# Other modification present
files <- c(system.file("extdata/modkit/Hypo1.first50Bed.txt",package = "bsseq"))
bsseq_nano <- read.modkit(files, rmZeroCov = FALSE, strandCollapse=FALSE)

hansenlab/bsseq documentation built on Nov. 6, 2024, 2:59 p.m.