BiFET identifies TFs whose footprints are overrepresented 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 pvalue as the probability of observing t_k or more target regions with footprints under the null hypothesis.
Package details 


Author  Ahrim Youn [aut, cre], Eladio Marquez [aut], Nathan Lawlor [aut], Michael Stitzel [aut], Duygu Ucar [aut] 
Bioconductor views  ATACSeq DNaseSeq Epigenetics GeneRegulation Genetics RIPSeq Software Transcription 
Date of publication  20180715 
Maintainer  Ahrim Youn <[email protected]> 
License  GPL3 
Version  1.0.1 
Package repository  View on Bioconductor 
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