ecoligenome.operon          package:ecolitk          R Documentation

_K_n_o_w_n _o_p_e_r_o_n _i_n _E._c_o_l_i - _d_a_t_a._f_r_a_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     The known operon in the Escherichia coli genome.

_U_s_a_g_e:

     data(ecoligenome.operon)

_F_o_r_m_a_t:

     A data frame with 932 observations (genes) on the following 4
     variables.

     _g_e_n_e._n_a_m_e a character vector

     _g_e_n_e._a_n_n_o_t_a_t_i_o_n a character vector

     _o_p_e_r_o_n._n_a_m_e a factor with levels the names of the operons

     _o_p_e_r_o_n._c_o_m_m_e_n_t_s a factor with levels the comments for the operons

_D_e_t_a_i_l_s:

     For some operons, the source of information specifies the
     existence of regulating elements such as promoter, terminator,
     box, etc... In those cases, the 'gene.name' is set to
     '"Regulation"', and the 'gene.annotation' gives what kind of
     regulating element it is. If volonteers, it would be neat to map
     those on the genome... Besides that, not much to add. The data
     structure is fairly straightforward.

_S_o_u_r_c_e:

     Built from the webpage: <URL:
     http://www.cib.nig.ac.jp/dda/backup/taitoh/ecoli.operon.html>

_E_x_a_m_p_l_e_s:

     library(Biobase)
     data(ecoligenome.operon)
     data(ecoligenomeSYMBOL2AFFY)

     ## something that might be useful when working with Affymetrix data:
     ## get the Affymetrix identifiers for the probe sets bundled in operons
     ## (see the vignette for more details)
     ecoligenome.operon$affyid <-
     unname(unlist(mget(ecoligenome.operon$gene.name,
                        ecoligenomeSYMBOL2AFFY, ifnotfound=NA)))

