DESCRIPTION

Package: BiFET
Type: Package
Title: Bias-free Footprint Enrichment Test
Version: 1.1.8
Date: 2018-07-10
Authors@R: c(person("Ahrim", "Youn", email = "Ahrim.Youn@jax.org",
    role = c("aut", "cre")), person("Eladio", "Marquez",
    email = "Eladio.Marquez@jax.org", role = c("aut")), 
    person("Nathan",  "Lawlor", email = "nathan.lawlor03@gmail.com", 
    role = c("aut")), person("Michael", "Stitzel",
    email = "Michael.Stitzel@jax.org", role = c("aut")),person("Duygu",
    "Ucar", email = "Duygu.Ucar@jax.org", role = c("aut")))
Maintainer: Ahrim Youn <Ahrim.Youn@jax.org>
Description: BiFET identifies TFs whose footprints are over-represented in
    target regions compared to background regions after correcting for the
    bias arising from the imbalance in read counts and GC contents between
    the target and background regions. For a given TF k, BiFET tests the null
    hypothesis that the target regions have the same probability of having
    footprints for the TF k as the background regions while correcting for
    the read count and GC content bias. For this, we use the number of target
    regions with footprints for TF k, t_k as a test statistic and calculate
    the p-value as the probability of observing t_k or more target regions
    with footprints under the null hypothesis.
License: GPL-3
biocViews: Genetics, Epigenetics, Transcription, GeneRegulation,
    ATACSeq, DNaseSeq, RIPSeq, Software
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: stats, poibin, GenomicRanges
Suggests: testthat, knitr
VignetteBuilder: knitr