Function reference • shaman

Data processing
`shaman_shuffle_hic_track()`	generate an expected hic track based on observed hic data
`shaman_score_hic_track()`	generate a score hic track based on observed and expected (shuffled) hic data
`shaman_shuffle_and_score_hic_mat()`	Inline function for generating an expected matrix and computing the score for a given interval
`shaman_score_hic_points()`	generate a score matrix for observed data based on the expected for a given set of points
`shaman_score_hic_mat()`	generate a score matrix for observed data based on the expected for a given 2D focus interval
`shaman_kk_norm()`	Compute a score matrix for observed data based on the expected for a given set of points
`shaman_generate_feature_grid()`	Calculate spatial enrichment of contacts between two features
Visualization Methods for graphical visualizing
`shaman_plot_map_score_with_annotations()`	plots hic normalized map with annotations
`shaman_gplot_map_score()`	plot a normlized hic map
`shaman_gplot_map()`	plot an observed or expected hic map
`shaman_plot_feature_grid()`	Plot spatial enrichment of contacts between two features
`shaman_score_pal()`	Returns the color palette used to display normalized scores
configuration Parameter configuration utility functions
`shaman_get_test_track_db()`	returns test misha db
`get_param_list()`	Get params from saved var
`get_param()`	Get params from saved var
`init_params()`	Read params from files

Reference