sample_alri: Randomly selects cells for artificial long range...

In rz6/DIADEM: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

Toghether with DIADEM::simulate_map.HiCglm function this can be used to create Hi-C contact maps with artificial long range differential interactions (see examples).

Usage

sample_alri(
  mtx,
  N = 100,
  max.diag = NA,
  radius = 1,
  alri.min.dist = 2 * radius + 1
)

Arguments

mtx	numeric Hi-C contact map in dense format
N	numeric number of cells to sample
max.diag	numeric specifies diagonal range to sample interactions from
radius	numeric number of cells to include in artificial interaction around (left, right, bottom, top or corners) with sampled interaction
alri.min.dist	numeric minimum distance (in number of cells left, right, bottom, top or diagonally) between any pair of sampled interactions (between their centers)

Details

Interaction is a square centered on i,j with height i - radius, ..., i, ..., i + radius and width j - radius, ..., j, ..., j + radius

The minmum distance between any pair of interactions alri.min.dist is measured as Euclidean distance between centers of 2 intractions (like i1, j1 and i2, j2)

Value

matrix with id, i, j columns indicating artificial long range interactions

rz6/DIADEM documentation built on Dec. 31, 2019, 3:51 a.m.