sim.mutants: Simulate data for a random transposon mutagenesis experiment
In negenes: Estimating the Number of Essential Genes in a Genome

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/sim_mutants.R

Simulate data for a random transposon mutagenesis experiment.

1	sim.mutants(n.sites, essential, n.sites2 = NULL, n.mutants)

`n.sites`	A vector specifying the number of transposon insertion sites in each gene. All elements must by strictly positive.
`essential`	A vector containing 1's (indicating that the corresponding gene is essential) and 0's (indicating that the corresponding gene is not essential). Must be the same length as `n.sites`.
`n.sites2`	A vector specfying the number of transposon insertion sites shared by adjacent genes. The ith element is the number of insertion sites shared by genes i and i+1. The last element is for sites shared by genes N and 1. If missing, these are assumed to be all 0.
`n.mutants`	Number of mutants to simulate.

If n.sites2 is missing or contains all 0's, a vector is returned containing the number of mutants observed for each gene.

If n.sites2 is not missing and has some positive entries, a matrix with two columns is returned. The first column contains the number of mutants observed for each gene alone; the second column contains the number of mutants observed shared by adjacent genes.

Karl W Broman, broman@wisc.edu

Blades, N. J. and Broman, K. W. (2002) Estimating the number of essential genes in a genome by random transposon mutagenesis. Technical Report MS02-20, Department of Biostatistics, Johns Hopkins University, Baltimore, MD. https://www.biostat.wisc.edu/~kbroman/publications/ms0220.pdf

negenes::negenes(), negenes::Mtb80()

## Not run: data(Mtb80)

# simulate 44% of genes to be essential
essential <- rep(0,nrow(Mtb80))
essential[sample(1:nrow(Mtb80),ceiling(nrow(Mtb80)*0.44))] <- 1

# simulate 759 mutants
counts <- sim.mutants(Mtb80[,1], essential, Mtb80[,2], 759)

# run the Gibbs sampler
output <- negenes(Mtb80[,1], counts[,1], Mtb80[,2], counts[,2])
## End(Not run)