Mtb80                package:negenes                R Documentation

_N_u_m_b_e_r _o_f _i_n_s_e_r_t_i_o_n _s_i_t_e_s _i_n _e_a_c_h _g_e_n_e _i_n _M _t_b _C_D_C_1_5_5_1

_D_e_s_c_r_i_p_t_i_o_n:

     Number of insertion sites in the initial 80% of each gene in the
     _Mycobacterium tuberculosis_ CDC1551 genome.

_U_s_a_g_e:

     data(Mtb80)

_F_o_r_m_a_t:

     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.

_S_o_u_r_c_e:

     <URL: http://www.tigr.org>

_R_e_f_e_r_e_n_c_e_s:

     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. <URL:
     http://www.biostat.biostat.wisc.edu/~kbroman/publications/ms0220.pdf>

_S_e_e _A_l_s_o:

     'negenes', 'sim.mutants'

_E_x_a_m_p_l_e_s:

     ## 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)

