shaman_score_hic_mat_for_track | R Documentation |
shaman_score_hic_mat_for_track
shaman_score_hic_mat_for_track( track_db, work_dir, obs_track_nms, exp_track_nms, points_track_nms, chrom, start1, end1, start2, end2, expand = 2000000, k = 100, min_dist = 1024 )
track_db |
Directory of the misha database. |
work_dir |
Centralized directory to store temporary files. |
obs_track_nms |
Names of observed 2D genomic tracks for the hic data. Pooling of multiple observed tracks is supported. |
exp_track_nms |
Names of expected (shuffled) 2D genomic tracks. Pooling of multiple expected tracks is supported. |
points_track_nms |
Names of 2D genomic tracks that contain points on which to compute normalized score. Pooling points from multiple tracks is supported. |
chrom |
The chormosome of the matrix. |
start1 |
The start coordinate of the first dimension. |
end1 |
The end coordinate of the first dimension. |
start2 |
The start coordinate of the second dimension. |
end2 |
The end coordinate of the second dimension. |
expand |
Size of expansion, points to include outside the matrix for accurate computing of the score. Note that for each observed point, its k-nearest neighbors must be included in the expanded matrix. |
k |
The number of neighbor distances used for the score. For higher resolution maps, increase k. For lower resolution maps, decrease k. |
min_dist |
The minimum distance between points. |
This function extracts observed data and expected data in an expanded matrix and computes The score for a point is the KS D-statistic of the distances to the points k-nearest-neighbors
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