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 |