excludeDoubleMatchingProbes  package:GeneRegionScan  R Documentation

_E_x_c_l_u_d_e _P_r_o_b_e_L_e_v_e_l_S_e_t _p_r_o_b_e_s _t_h_a_t _m_a_t_c_h _m_o_r_e _t_h_a_n _o_n_c_e _i_n _g_e_n_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     Function that will remove probes from ProbeLevelSet if they have
     more than one match in a given genome.

_U_s_a_g_e:

         excludeDoubleMatchingProbes(object, genome="BSgenome.Hsapiens.UCSC.hg18", verbose=TRUE,
         directions=c("matchForwardSense", "matchForwardAntisense", "matchReverseSense", "matchReverseAntisense"),
         previousData = NULL)

_A_r_g_u_m_e_n_t_s:

  object: A ProbeLevelSet class object.

  genome: character string with the name of the BSGenome in which
          sequences should be found. Defaults to the human genome.

 verbose: TRUE or FALSE.

directions: character string with elements from c("matchForwardSense",
          "matchForwardAntisense", "matchReverseSense",
          "matchReverseAntisense"). Defines which directions
          (complementary and reverse mirrorings) that should be
          scanned. Defaults to all directions.

previousData: Optional: The output from a call to findSequenceInGenome.
          If given the scanning will be skipped, and the probes will be
          omitted directly. Useful in cases were datasets from the same
          region needs to be processed.

_D_e_t_a_i_l_s:

     This function will take quite a while to run, so if you have many
     sequences, overnight runs are recommended.  BSgenome contains some
     alternative versions of chromosomes. They are marked with an
     underscore. This function  automatically disregards chromosome
     names with an underscore, and this is known to work for the human
     genome. Nevertheless,  check the output printed to terminal if all
     chromosomes are included. The function is a wrapper around
     findSequenceInGenome,  which can be used for purposes that are
     more flexible (although that function really is just following the
     example in the BSgenome package)

     At present, there is no functionality to check matches with known
     SNP or known splice forms taken into account.

_V_a_l_u_e:

     The ProbeLevelSet class object provided as argument, with all
     double matching probes removed. Double matching probes are probes
     whose sequence are found twice or more in the genome. In addition,
     the output of the matching investigation is saved in the notes of
     the ProbeLevelSet and can be further examined for information on
     the locations of the probe sequences in relation to the BSgenome
     sequences.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'findSequenceInGenome', 'BSgenome', 'excludeDoubleMatchingProbes'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #you can run this, but it takes a lot of time
             probelevelsetwithnodoubles<-excludeDoubleMatchingProbes(probelevelset)
             
     ## End(Not run)

