OptRange: Number of significant targets

In takahirosuzuki0626/mTFTarget:

Description

This function compute the number of significant targets of methyl-regulating TFs in differentranges. Number of motifs in a region is dependent of the rength of the region. To potimize the range of the region, this function return the number of significatn targets changing the range. Becaue fitting function is not robust to outliers, if a fitting return the error, repret the fitting by 100 times. output figures consist of histgram of motif number at DMR and at random regions, fitting model line plot for each results. and return tabel of the result

Usage

OptRange(infile = infile, motifDBList = motifDBList,
  ControlColnum = ControlColnum, TreatmentColnum = TreatmentColnum,
  MethylDemethyl = MethylDemethyl, version = version,
  outname = outname, nbiom_cutoff = nbiom_cutoff, ranges)

Arguments

infile	input m-value file
motifDBList	list of motif PWM
ControlColnum	control column index(s)
TreatmentColnum	treatment column index(s)
MethylDemethyl	Metylation or Demethylation analysis
version	version of methylation array 450 or EPIC(850)
outname	output file name
nbiom_cutoff	cutoff p-value for negative binomial test
ranges	a vector. ranegs to be tested.

Value

a matrix of results of fitting and negative binominal test

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