singleCell {SITH} | R Documentation |
Simulate single cell sequencing data
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 |
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 <philnicol740@gmail.com>
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)