Skip to contents

run_methyltfr

Source: R/run_methyltfr.R
run_methyltfr.Rd

This function is a wrapper function to calculate the deviation in transcription factor footprint base for all given motifs per raw samples

Usage

run_methyltfr(
  sample_ann,
  sample_dir,
  tf_bindsites = NULL,
  gcfreqs = NULL,
  gc_dist = NULL,
  sampleColName = "bedFile",
  chunkSize = 20,
  full_path = FALSE,
  annfile = NULL,
  threads = 1,
  enhancer = NULL,
  filetype = NULL,
  ignoreStrand = TRUE,
  cov_threshold = 1
)

Arguments

sample_ann

A tab seperated file contains sample annotations

sample_dir

The directory where all bed file and annotation file stored

tf_bindsites

a GRangesList object contains tf binding sites positions

gcfreqs

a list of GC bin frequency tables (matrices for multiple motif)

gc_dist

a GRanges object contains Genome wide GC distribution

sampleColName

column name of the sample bed file in the annotation file

chunkSize

Chunk size for parallel processing of motifs (default: 20)

full_path

if TRUE, the bed file path in the annotation file is full path

annfile

if provided, the sample annotation file is not read from the sample_dir

threads

Thread count for parallel processing

enhancer

a GRanges object specifying regions such as distal motif (optional)

filetype

file type of the bed file, currently supported: bissnp,epp,allc,bismarkcytosine,bismarkcov,encode

ignoreStrand

if TRUE, it ignores strand info from annotation

cov_threshold

  • numeric, coverage threshold to filter out low coverage sites, default is 1

Value

a methylTFRdeviations object with bias-corrected deviation and Z-scores