R/shaman.R
shaman_score_hic_points.Rdshaman_score_hic_points
shaman_score_hic_points(
obs_track_nms,
exp_track_nms,
points,
regional_interval,
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.
A score will be computed for each of the points.
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.
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.
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
points <- gextract("hic_obs", gintervals.2d(2, 175.5e06, 177.5e06, 2, 175.5e06, 177.5e06), band = c(-2e06, -1024))
#> Error: Invalid interval (chr2, 1.755e+08, 1.775e+08): end coordinate exceeds chromosome boundaries
mat_score <- shaman_score_hic_points(
obs_track_nms = "hic_obs", exp_track_nms = "hic_exp",
points = points, regional_interval = gintervals.2d(2, 175e06, 178e06, 2, 175e06, 178e06)
)
#> obs = hic_obs
#> Error: Invalid interval (chr2, 1.75e+08, 1.78e+08): end coordinate exceeds chromosome boundaries
shaman_gplot_map_score(mat_score$points)
#> Error in is.data.frame(x): object 'mat_score' not found