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
)

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
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 consdered for switching
grid_high: Final size of maximum distance between contact pairs consdered for switching
grid_increase: Grid increase size
grid_step_iter: Number of iterations in each grid size

Value

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. 4) exp_fn - the name of the expected (shuffled) data file

Details

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

Examples


# Set misha db to test
gsetroot(shaman_get_test_track_db())
#> Error in setwd(groot): cannot change working directory
mat_score <- shaman_shuffle_and_score_hic_mat(
    obs_track_nms = "hic_obs",
    interval = gintervals.2d(2, 175.5e06, 177.5e06, 2, 175.5e06, 177.5e06),
    expand = 5e05,
    work_dir = tempdir()
)
#> 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