sim.mutants {negenes} | R Documentation |
Simulate data for a random transposon mutagenesis experiment.
sim.mutants(n.sites, essential, n.sites2, 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, kbroman@biostat.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. http://www.biostat.biostat.wisc.edu/~kbroman/publications/ms0220.pdf
## 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)