methyltfr_core

Internal engine shared by run_methyltfr and run_methylTFR_RnBeads. It validates the motif set, allocates the on-disk sinks, iterates over samples, computes per-motif deviations in chunks and assembles the resulting methylTFRdeviations object.

The only difference between the two public entry points is where the per-sample methylation calls come from. That difference is isolated in the msites_fun argument, so both entry points share identical numerical behaviour.

Usage

methyltfr_core(
  sample_ids,
  msites_fun,
  samples,
  tf_bindsites,
  gcfreqs,
  gc_dist,
  chunkSize = 20,
  threads = 1,
  enhancer = NULL,
  ignoreStrand = TRUE
)

Arguments

sample_ids

A character vector of sample identifiers. Used for the column names of the resulting object and to size the sinks.

msites_fun

A function of a single integer i returning a GRanges object of methylation calls for sample i, with a numeric score metadata column holding methylation levels in [0, 1].

samples

A data.frame of sample annotation with one row per entry of sample_ids, used as colData.

tf_bindsites

a GRangesList object containing TF binding site positions.

gcfreqs

a list of GC bin frequency tables.

gc_dist

a GRanges object containing the genome-wide GC distribution.

chunkSize

Chunk size for parallel processing of motifs.

threads

Thread count for parallel processing.

enhancer

a GRanges object restricting the analysis to a set of regions such as distal regulatory elements (optional).

ignoreStrand

if TRUE, strand information is ignored.

Value

a methylTFRdeviations object with bias-corrected deviations, row-wise Z-scores and expected deviations.