Function reference • preciseTAD

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`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.
`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
`tfbsList`	A list of the chromosomal coordinates for 26 transcription factor binding sites from the Gm12878 cell line

Reference

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