validProbeAnno             package:Ringo             R Documentation

_F_u_n_c_t_i_o_n _t_o _c_h_e_c_k _a _p_r_o_b_e_A_n_n_o _e_n_v_i_r_o_n_m_e_n_t

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

     This function checks whether a probeAnno environment seems to be
     valid and will work with other Ringo functions.

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

     validProbeAnno(probeAnno)

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

probeAnno: an environment that holds probe matches to genomic
          coordinates

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

     This function checks certain properties of the mapping environment
     that are used by other Ringo functions. It can indicate potential
     problems in the environment.

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

     'TRUE' if the environment seems to be a valid probeAnno
     environment, 'FALSE' if a potential problems with this environment
     was identified. This potential problem is explained as a warning.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'posToProbeAnno'

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

      ## first a toy example:
      if (interactive()){
       A = new.env()
       assign("1.+.start",seq(100,1000,by=100),env=A)
       validProbeAnno(A)
       assign("1.+.end",c(99,seq(250,1050,by=100)),env=A)
       assign("1.+.unique",numeric(10),env=A)
       assign("1.+.index",c(2:5,1,7,8,6,10), env=A)
       validProbeAnno(A)
       assign("1.+.index",c(2:5,1,7,8,6,10,3), env=A)
       validProbeAnno(A)
       assign("1.+.end",c(150,seq(250,1050,by=100)),env=A)
       validProbeAnno(A)
      } 
      ## validate the provided example probeAnno
      load(file.path(system.file("exData",package="Ringo"),"exampleProbeAnno.rda"))
      validProbeAnno(exProbeAnno)

