# preciseTAD: A machine learning framework for precise TAD boundary prediction

## Documentation for package ‘preciseTAD’ version 1.4.0

- 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