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Table 1 Functions in the target R package

From: Integrating binding and expression data to predict transcription factors combined function

Function Description Input Output
merge_ranges Merge overlapping peaks & regions. peaks & regions Merged ranges
find_distance Calculate the distance between the centers of peaks & regions. peaks & regions Distances
score_peaks Calculate regulatory scores for peaks in relation to regions. Distances Peak scores
score_regions Calculate regulatory scores for regions. Peak scores & region IDs Regions scores
rank_product Rank regions based on the regulatory potential & expression statistics. Regions scores, expression statistics & region IDs Regions rank products
associated_peaks Select overlapping peaks & regions & calculate a score for each peak in relation to a region. peaks & regions Assigned peaks
direct_target Select & rank regions with overlapping peaks. peaks & regions Assigned targets
plot_predictions Plot the ECDF of the regions’ ranks by group. Ranks & group factor ECDF plot
test_predictions Test the ECDF of the ranks in the regions in each group are from different distribution. Ranks & group factor t-statistics & p-values