shaman_shuffle_and_score_hic_mat: Inline function for generating an expected matrix and...

In tanaylab/shaman: shaman - Sampling HiC contAct Matrices for Aparametric Normalization

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

Description

shaman_shuffle_and_score_hic_mat

Usage

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

Details

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

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

Examples

# Set misha db to test
gsetroot(shaman_get_test_track_db())
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()
)
shaman_gplot_map_score(mat_score$points)

tanaylab/shaman documentation built on April 2, 2022, 1:32 a.m.