occup2Negenes            package:occugene            R Documentation

_C_o_n_v_e_r_t _O_c_c_u_p_a_n_c_y _F_o_r_m_a_t _t_o _N_e_g_e_n_e_s

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

     Convert the annotation and insertion formation of the occupancy
     package into the format for the negenes package.

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

     occup2Negenes(anno,clone,INTERGENIC=FALSE)

_A_r_g_u_m_e_n_t_s:

    anno: 2-column matrix of annotation

   clone: vector of insertion locations

INTERGENIC: Process the intergenic region as last ORF.

_D_e_t_a_i_l_s:

     Convert the annotation and insertion formation of the occupancy
     package into the format for the negenes package. Of the returned
     data frame, column 1 is  n.sites, column 2, n.sites2, column 3,
     counts, column 4, counts2.

_V_a_l_u_e:

     Returns a data frame

_A_u_t_h_o_r(_s):

     Oliver Will owill4@yahoo.com

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

     See the book chapter O. Will (**) in **

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

     data(sampleAnnotation)
     data(sampleInsertions)
     anno <- cbind(sampleAnnotation$first,sampleAnnotation$last)
     clone <- sampleInsertions$position
     occup2Negenes(anno,clone)

