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 |