Deviation scores of a ChrAccR dataset

The ATAC counterpart of run_methyltfr. The methylTFR annotation is used unchanged, methylation levels are replaced by insertion densities per base and per site, and the expected profile comes from the GC bin composition of the binding sites.

Usage

runChromTFR(
  dsa,
  tf_bindsites = NULL,
  gcfreqs = NULL,
  gc_dist = NULL,
  sampleIds = NULL,
  motifs = NULL,
  regions = NULL,
  enhancer = NULL,
  threads = 1,
  ignoreStrand = TRUE,
  shift = c(4L, -5L),
  normalize = TRUE,
  sample_ann = NULL
)

Arguments

dsa

A DsATAC object or the path of a ChrAccR dataset.

tf_bindsites

A GRangesList of binding site positions.

gcfreqs

A list of GC bin frequency tables.

gc_dist

A GRanges of the genome wide GC distribution.

sampleIds

Samples to process, all of them by default.

motifs

Motifs to process, all of them by default.

regions

Optional GRanges restricting the insertions.

enhancer

Optional GRanges restricting the binding sites.

threads

Thread count for parallel processing.

ignoreStrand

If TRUE, strand information is ignored.

shift

Offsets applied to the forward and reverse fragment ends.

normalize

If TRUE, counts are scaled to insertions per million.

sample_ann

Optional data.frame of sample annotation.

Value

A SummarizedExperiment with the deviations, their row-wise z-scores and the expected deviations.

Examples

if (FALSE) { # \dontrun{
devs <- runChromTFR(dsa, tf_bindsites, gcfreqs, gc_dist)
} # }