bsseq_to_log_methy_ratio: Convert BSseq object to log-methylation-ratio matrix

In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

Convert BSseq object to log-methylation-ratio matrix

Description

Creates a log-methylation-ratio matrix from a BSseq object that is useful for dimensionality reduction plots.

Usage

bsseq_to_log_methy_ratio(
  bsseq,
  regions = NULL,
  prior_count = 2,
  drop_na = TRUE
)

Arguments

bsseq	the BSseq object.
regions	the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per site.
prior_count	the prior count added to avoid taking log of 0.
drop_na	whether to drop rows with all NA values.

Value

a matrix containing log-methylation-ratios.

Examples

nmr <- load_example_nanomethresult()
bsseq <- methy_to_bsseq(nmr)
regions <- exons_to_genes(NanoMethViz::exons(nmr))
log_m_ratio <- bsseq_to_log_methy_ratio(bsseq, regions)

Shians/NanoMethViz documentation built on Dec. 17, 2024, 8:56 a.m.