Inline function for generating an expected matrix and computing the score for a given interval — shaman_shuffle_and_score_hic

shaman_shuffle_and_score_hic_mat

shaman_shuffle_and_score_hic_mat(
  obs_track_nms,
  interval,
  work_dir,
  expand = 1000000,
  min_dist = 1024,
  k = 100,
  dist_resolution = NA,
  decay_smooth = NA,
  hic_mcmc_max_resolution = 400,
  shuffle = 80,
  grid_small = 500000,
  grid_high = 1000000,
  grid_increase = 500000,
  grid_step_iter = 40,
  seed = NULL
)

Arguments

obs_track_nms: Name of observed 2D genomic tracks for the hic data.
interval: 2D interval on which to compute the scores.
work_dir: Centralized directory to store temporary files.
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.
min_dist: The minimum distance between points.
k: The number of neighbor distances used for the score. For higher resolution maps, increase k. For lower resolution maps, decrease k.
dist_resolution: Number of bins in each log2 distance unit. If NA, value is determined based on observed data (recommended).
decay_smooth: Number of bins to use for smoothing the MCMC target function: the decay curve. If NA, value is determined based on observed data (recommended).
hic_mcmc_max_resolution: Maximum number of bins for each log2 unit.
shuffle: Number of shuffling rounds for each observed point.
grid_small: Initial size of maximum distance between contact pairs considered for switching
grid_high: Final size of maximum distance between contact pairs considered for switching
grid_increase: Grid increase size
grid_step_iter: Number of iterations in each grid size
seed: Seed for the shuffler: NULL (default) seeds it from the current time (in seconds), or a whole number between 0 and 2^31 - 1. The shuffler prints the seed it uses.

Value

NULL if insufficient observed data, otherwise returns a list containing: 1) points - start1, start2 and score for all observed points. 2) obs - the observed points. 3) exp - the expected points. 4) exp_fn - the name of the expected (shuffled) data file 5) seed - the seed the shuffler used

Details

This function generates an expected 2D hic matrix based on observed hic data, and computes its score.

Examples


# Set misha db to test
library(misha)
gsetroot(shaman_get_test_track_db())
mat_score <- shaman_shuffle_and_score_hic_mat(
    obs_track_nms = "hic_obs",
    interval = gintervals.2d(2, 176.6e06, 176.9e06, 2, 176.6e06, 176.9e06),
    expand = 1e05,
    work_dir = tempdir(),
    shuffle = 2, # default is set to 80
    grid_step_iter = 1, # default is set to 40
    seed = 1
)
#> working on  21760 points
#> adjusting expand
#> combining multi tracks
#> replicating multi-contacts
#> shuffling 97618 observed points
#> going into knn with 97618 observed and 195236 expected
#> going into shuffled knn
shaman_gplot_map_score(mat_score$points)