sample: Sample cells from a population

sample_uniform_regionsR Documentation

Sample cells from a population

Description

Sample cells from a population

Usage

sample_uniform_regions(tbl, nsam = 2L, ncell = 10L, jitter = 0)

sample_random_regions(tbl, nsam = 2L, ncell = 10L)

sample_bulk(tbl, center = c(x = 0, y = 0, z = 0), ncell = 10L)

sim_sample_single_cell(graph, nrep = 1L, ncell = 100L, mu = 0, accel = 0)

sim_sample_biopsy(
  graph,
  population,
  nrep = 1L,
  nsam = 5L,
  ncell = 100L,
  mu = 0,
  accel = 0
)

evaluate_mrs(
  population,
  nsam,
  ncell,
  threshold = 0.05,
  sensitivity = 0.05,
  jitter = 0
)

distances_mrs(population, nsam, ncell, jitter = 0)

Arguments

tbl

tibble of extant cells with id, x, y, z columns

nsam

number of regions to sample

ncell

number of cells per specimen

jitter

amount of random variations on x and y axes

center

named (x, y, z) vector, list, or tibble

graph

igraph

nrep

number of replications.

mu

mutation rate per cell division (ignored if segsites is given)

accel

assumption undocumented yet

population

tbl

threshold

minimum frequency of detectable alleles

sensitivity

minimum allele frequency

Details

sample_uniform_regions sample uniformly distributed regions.

sample_random_regions samples multiple regions at random.

sample_bulk samples a bulk of cells near the specified center.

evaluate_mrs is a shortcut to evaluate multi-region sampling.

distances_mrs is a shortcut for sampling and calculation


heavywatal/rtumopp documentation built on Aug. 27, 2024, 11:50 a.m.