shaman - Sampling HiC contAct Matrices for Aparametric Normalization


[Up] [Top]

Documentation for package ‘shaman’ version 2.0

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