negenes (version 1.0-12)

Mtb80: Number of insertion sites in each gene in M tb CDC1551

Description

Number of insertion sites in the initial 80% of each gene in the Mycobacterium tuberculosis CDC1551 genome.

Format

A matrix with two columns. Each row corresponds to a gene. (The row names are the MT numbers of the genes.) The element in the first column is the number of transposon insertion sites in the initial 80% that appear in the corresponding gene and in no other gene. The element in the second column is the number of transposon insertion sites in the initial 80% of both that gene and the following gene. There are 4204 rows; the 46 genes with no such site are not included.

References

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

See Also

negenes::negenes(), negenes::sim.mutants()

Examples

# 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])
# }
# NOT RUN {
# }