MotPosiList: Motif position list at DMRs

In takahirosuzuki0626/mTFTarget:

Description

This function performes differentially methylation analysis and motif enrichment analysis at the DMR

Usage

MotPosiList(infile = "sel_processed_Mval.txt", motifDBList,
  ControlColnum, TreatmentColnum, p.cutoff = 0.001, cutoff = 2,
  MethylDemethyl = "Demethyl", version = "850", sampling = FALSE,
  seq_range = c(-200, 200), outname = "motif_num_dist",
  nbiom_cutoff = 0.05)

Arguments

infile	input m-value file
motifDBList	list of motif PWM
ControlColnum	control column index(s)
TreatmentColnum	treatment column index(s)
p.cutoff	cutoff for multi-sample comarison (p-value)
cutoff	cutoff for single sample comparison (delta M)
MethylDemethyl	Metylation or Demethylation analysis
version	version of methylation array 450 or EPIC(850)
sampling	number of sampling. if FALSE, use all data
seq_range	range from CpG to be analyzed
outname	output file name
nbiom_cutoff	cutoff of negative binomial model test

Value

a List of lists of motif positions in DMR from CpG sites and of that in random regions

takahirosuzuki0626/mTFTarget documentation built on Jan. 4, 2022, 9:44 a.m.