singleCell: Simulate single cell sequencing data

In SITH: A Spatial Model of Intra-Tumor Heterogeneity

Description

Simulate single cell sequencing data by selecting a cell at a specified position

Usage

singleCell(tumor, pos, noise = 0)

Arguments

tumor	A list which is the output of simulateTumor().
pos	A vector of length 3 giving the (x,y,z) coordinates of the cell to sample.
noise	The false negative rate.

Details

This function selects the cell at pos (error if no cell at specified position exists) and returns the list of mutations present in the cell. Due to technological artifacts, the false negative rate can be quite higher (10-20 percent). To account for this, the noise parameter introduces false negatives into the data set at the specified rate.

Value

A data frame with 1 row and columns corresponding to the mutations present in the cell. A 1 indicates that the mutation is detected while a 0 indicates the mutation is not detected.

Author(s)

Phillip B. Nicol <[e-mail]>

References

K. Jahn, J. Kupiers and N. Beerenwinkel. Tree inference for single-cell data. Genome Biology, volume 17, 2016. https://doi.org/10.1186/s13059-016-0936-x.

Examples

set.seed(1126490984)
out <- simulateTumor(max_pop = 1000)
df <- singleCell(tumor = out, pos = c(0,0,0), noise = 0.1)

SITH documentation built on Jan. 5, 2021, 5:08 p.m.