R/shaman.R
shaman_score_hic_mat.Rdshaman_score_hic_mat
shaman_score_hic_mat(
obs_track_nms,
exp_track_nms,
focus_interval,
regional_interval,
points_track_nms = obs_track_nms,
min_dist = 1024,
k = 100,
k_exp = 2 * k
)Names of observed 2D genomic tracks for the hic data. Pooling of multiple observed tracks is supported.
Names of expected (shuffled) 2D genomic tracks. Pooling of multiple expected tracks is supported.
2D interval on which to compute the scores.
An expansion of the focus interval, inclusing points outside the focus matrix for accurate computing of the score. Note that for each observed point, its k-nearest neighbors must be included in the expanded matrix.
Names of 2D genomic tracks that contain points on which to compute normalized score. Pooling points from multiple tracks is supported.
The minimum distance between points.
The number of neighbor distances used for the score. For higher resolution maps, increase k. For lower resolution maps, decrease k.
The number of neighbor distances used for the score on the expected tracks. Note, that when comparing expected generated by shuffling the observed, k_exp should be 2*k as the number of contacts in the expected track will always be twice the observed. However, if comparing between two datasets that are independent, k_exp should be set to NA and the will be determined by the ratio between the total number of contacts in this region.
NULL if insufficient observed data, otherwise resturns a list containing 3 elements: 1) points - start1, start2 and score for all observed points. 2) obs - the observed points. 3) exp - the expected 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
# Set misha db to test
gsetroot(shaman_get_test_track_db())
#> Error in setwd(groot): cannot change working directory
mat_score <- shaman_score_hic_mat(
obs_track_nms = "hic_obs", exp_track_nms = "hic_exp",
focus_interval = gintervals.2d(2, 175.5e06, 177.5e06, 2, 175.5e06, 177.5e06),
regional_interval = gintervals.2d(2, 175e06, 178e06, 2, 175e06, 178e06)
)
#> Error: Invalid interval (chr2, 1.755e+08, 1.775e+08): end coordinate exceeds chromosome boundaries
shaman_gplot_map_score(mat_score$points)
#> Error in is.data.frame(x): object 'mat_score' not found