MotScr: PWM overrepresentation analysis pipline for illumina...

In takahirosuzuki1980/InfiniumDiffMetMotR: Motif Overrepresentation analysis for Illumina Methylation Arrays

Description

pipline to analyze enrichment of given motif PWMs for differentially methylated region based on Illumina infinium methylation array data.

Usage

MotScr(infile, motifDBList, cutoff = 2, p.cutoff = 0.001,
  outname = "screening_result", ControlColnum, TreatmentColnum,
  MethylDemethyl = "Demethyl", version = "850", sampling = FALSE)

Arguments

infile	input file: normalized M-value matrix
motifDBList	PWM data list
cutoff	cutoff for delta-M-value
p.cutoff	cutoff for Welch's t-test
outname	output files ID
ControlColnum	column number for Control sample(s)
TreatmentColnum	column number for target sample(s)
MethylDemethyl	direction of Ddifferentially methylated regions (methylated or demethylated)
version	version of Infinium Methjylation array (450 or 850(orEPIC))
sampling	If sampling number is indicated and DMP is more than sampling number, analysis is ran with randomly selected DMP. If FALSE, all DMPs are analyzed.

Value

analysis summary files and plots, Rdata

takahirosuzuki1980/InfiniumDiffMetMotR documentation built on March 31, 2021, 8:41 a.m.