findDupMarkers              package:qtl              R Documentation

_F_i_n_d _m_a_r_k_e_r_s _w_i_t_h _i_d_e_n_t_i_c_a_l _g_e_n_o_t_y_p_e _d_a_t_a

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

     Identify sets of markers with identical genotype data.

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

     findDupMarkers(cross, chr, exact.only=TRUE, adjacent.only=FALSE)

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

   cross: An object of class 'cross'.  See 'read.cross' for details.

     chr: Optional vector specifying which chromosomes to consider.
          This may be a logical, numeric, or character string vector.

exact.only: If TRUE, look only for markers that have matching genotypes
          and the same pattern of missing data; if FALSE, also look for
          cases where one the observed genotypes at marker match those
          at another, and where the first marker has missing genotype
          whenever the genotype for the second marker is missing.

adjacent.only: If TRUE, look only for sets of markers that are adjacent
          to each other.

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

     If 'exact.only=TRUE', we look only for groups of markers whose
     pattern of missing data and observed genotypes match exactly.  One
     marker (chosen at random) is selected as the name of the group (in
     the output of the function).

     If 'exact.only=FALSE', we look also for markers whose observed
     genotypes are contained in the observed genotypes of another
     marker.  We use a pair of nested loops, working from the markers
     with the most observed genotypes to the markers with the fewest
     observed genotypes.

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

     A list of marker names; each component is a set of markers whose
     genotypes match one other marker, and the name of the component is
     the name of the marker that they match.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'drop.nullmarkers', 'drop.markers'

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

     data(hyper)

     hyper <- drop.nullmarkers(hyper)

     dupmar <- findDupMarkers(hyper) # finds 4 pairs
     dupmar.adjonly <- findDupMarkers(hyper, adjacent.only=TRUE) # finds 4 pairs

     dupmar.nexact <- findDupMarkers(hyper, exact.only=FALSE, adjacent.only=TRUE) # finds 6 pairs

     # one might consider dropping the extra markers
     totmar(hyper) # 173 markers
     hyper <- drop.markers(hyper, unlist(dupmar.adjonly))
     totmar(hyper) # 169 markers

