preciseTAD: A machine learning framework for precise TAD boundary prediction

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Documentation for package ‘preciseTAD’ version 1.14.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

arrowhead_gm12878_5kb	Domain data from ARROWHEAD TAD-caller for GM12878 at 5 kb
bedToGRangesList	Function to create a GRangesList object from functional genomic annotation data in the form of BED files
binary_func	Helper function used to create binary overlap type feature space
count_func	Helper function used to create count overlap type feature space
createTADdata	Function to create a data matrix used for building a predictive model to classify boundary regions from functional genomic elements
distance_func	Helper function used to create (log2) distance type feature space
extractBoundaries	Function to extract boundaries from domain data.
juicer_func	Helper function for transforming a GRanges object into matrix form to be saved as .txt or .BED file and imported into juicer
percent_func	Helper function used to create percent overlap type feature space
preciseTAD	Precise TAD boundary prediction at base-level resolution using density-based spatial clustering and partitioning techniques
signal_func	Helper function used to create signal type feature space
TADrandomForest	A wrapper function passed to 'caret::train' to apply a random forest classification algorithm built and tested on user-defined binned domain data from 'createTADdata'.
TADrfe	A wrapper function passed to 'caret::rfe' to apply recursive feature elimination (RFE) on binned domain data as a feature reduction technique for random forests. Backward elimination is performed from p down to 2, by powers of 2, where p is the number of features in the data.
tfbsList	A list of the chromosomal coordinates for 26 transcription factor binding sites from the Gm12878 cell line