randomBulkSamples {SITH}

Simulate multi-region bulk sampling

Description

Simulate bulk sequencing data by taking a local sample from the tumor and computing the variant allele frequencies of the various mutations.

Usage

randomBulkSamples(
  tumor,
  nsamples,
  cube.length = 5,
  threshold = 0.05,
  coverage = 0
)

Arguments

tumor

A list which is the output of simulateTumor().

nsamples

The number of bulk samples to take.

cube.length

The side length of the cube of cells to be sampled.

threshold

Only mutations with an allele frequency greater than the threshold will be included in the sample.

coverage

If nonzero then deep sequencing with specified coverage is performed.

Details

This is the same as bulkSample(), except multiple samples are taken with random center points.

Value

A data frame with nsamples rows and columns corresponding to the mutations. The entries are the mutation allele frequency.

Author(s)

Phillip B. Nicol

Examples

out <- simulateTumor(max_pop = 1000)
df <- randomBulkSamples(tumor = out, nsamples = 5, cube.length = 5, threshold = 0.05)