shaman_shuffle_hic_mat_for_track: Generate an expected matrix from observed data as a process...

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

Generate an expected matrix from observed data as a process for generating an expected track

Description

shuffle_hic_mat_for_track

Usage

shaman_shuffle_hic_mat_for_track(
  track_db,
  track,
  work_dir,
  chrom,
  start1,
  end1,
  start2,
  end2,
  min_dist = 1024,
  max_dist = max(gintervals.all()$end),
  dist_resolution = NA,
  decay_smooth = NA,
  proposal_iterations = 10000000,
  shuffle = 80,
  hic_mcmc_max_resolution = 400,
  raw_ext = "raw",
  shuffled_ext = "shuffled",
  grid_small = 500000,
  grid_high = 1000000,
  grid_increase = 500000,
  grid_step_iter = 40,
  sort_uniq = FALSE
)

Arguments

track_db	Directory of the misha database.
track	Name of observed 2D genomic track for the hic data.
work_dir	Centralized directory to store temporary files.
chrom	The chormosome of the matrix.
start1	The start coordinate of the first dimension.
end1	The end coordinate of the first dimension.
start2	The start coordinate of the second dimension.
end2	The end coordinate of the second dimension.
min_dist	The minimum distance between contact end points.
max_dist	The maximum distance between contact end points.
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).
proposal_iterations	Number of MCMC sampling iterations between proposal corrections.
shuffle	Number of shuffling rounds for each observed point.
hic_mcmc_max_resolution	Maximum number of bins for each log2 unit
raw_ext	File extension of the observed data.
shuffled_ext	File extension of the shuffled data.
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
sort_uniq	Binary flag, indicating whether the shuffled matrix file should be sorted and contacts combined. This is required prior to importing the track to misha, and should be applied to full chromosomes only.

Details

This function generates an expected 2D hic matrix from observed hic data. Should not be called externally, The observed data is a combination of observed contacts in scope plus already shuffled near-cis contacts (stored in work_dir) which we sample from to maintain the decay probability curve.

Each step creates temporary files of the shuffled matrices which are then joined to a track. Temporary files are deleted upon track creation.

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