# shaman - Sampling HiC contAct Matrices for Aparametric Normalization

## Documentation for package ‘shaman’ version 2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

shaman-package | shaman.
ctcf_forward | Human CTCF motifs found on forward strand on hg19 genome
ctcf_reverse | Human CTCF motifs found on reverse strand on hg19 genome
get_param | Get params from saved var
get_param_list | Get params from saved var
init_params | Read params from files
shaman | shaman.
shaman_generate_feature_grid | Calculate spatial enrichment of contacts between two features
shaman_get_test_track_db | returns test misha db
shaman_gplot_map | plot an observed or expected hic map
shaman_gplot_map_score | plot a normlized hic map
shaman_kk_norm | Compute a score matrix for observed data based on the expected for a given set of points
shaman_plot_feature_grid | Plot spatial enrichment of contacts between two features
shaman_plot_map_score_with_annotations | plots hic normalized map with annotations
shaman_plot_tracks_and_annotations | plots misha 1D tracks and annotations
shaman_score_hic_mat | generate a score matrix for observed data based on the expected for a given 2D focus interval
shaman_score_hic_mat_for_track | generate a score matrix for observed data based on the expected
shaman_score_hic_points | generate a score matrix for observed data based on the expected for a given set of points
shaman_score_hic_track | generate a score hic track based on observed and expected (shuffled) hic data
shaman_score_pal | Returns the color palette used to display normalized scores
shaman_shuffle_and_score_hic_mat | Inline function for generating an expected matrix and computing the score for a given interval
shaman_shuffle_hic_mat_for_track | Generate an expected matrix from observed data as a process for generating an expected track
shaman_shuffle_hic_track | generate an expected hic track based on observed hic data