computeDeviation

computeDeviation is a function to calculate the deviation in transcription factor binding sites for a given motif

Usage

computeDeviation(
  motif,
  msites,
  tf_bindsites,
  gcfreqs,
  enhancer = NULL,
  ignoreStrand = TRUE,
  binMsites
)

Arguments

motif

A character vector containing motif name

msites

imported methylation sites

tf_bindsites

a GRangesList object contains tf binding sites positions

gcfreqs

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

enhancer

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

ignoreStrand

if TRUE, it ignores strand info from annotation

binMsites

A matrix object with GC bin with corresponding avg methylation

Value

a numeric deviation score for a given motif

Examples

library(methylTFR)

# Load the data
load(system.file("extdata",
    "BATF_tf_bindsites.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "example_data.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "BATF_gcfreqs.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "gcdist_subset.rda",
    package = "methylTFR"
))

# Compute binMsites
bin_meth <- addGCBintoMethylome(msites, gcdist, TRUE)

# Compute the deviation
devs <- computeDeviation("BATF",
    msites,
    tf_bindsites,
    gcfreqs,
    enhancer = NULL,
    ignoreStrand = TRUE,
    bin_meth
)