homozygote           package:GeneticsBase           R Documentation

_F_l_a_g _o_b_s_e_r_v_a_t_i_o_n_s _w_i_t_h _s_p_e_c_i_f_i_c _a_l_l_e_l_e _p_a_t_t_e_r_n_s

_D_e_s_c_r_i_p_t_i_o_n:

_h_o_m_o_z_y_g_o_t_e Flag observatsions with identical alleles

_h_e_t_e_r_o_z_y_g_o_t_e Flag observations with discordant alleles

_c_a_r_r_i_e_r Flag observations containing a specified allele

_d_o_m_i_n_a_n_t Flag observations containing one or more of the  specified
     alleles.

_r_e_c_e_s_s_i_v_e Flag observations containing only the  specified alleles.

_U_s_a_g_e:

     homozygote(object, ...)
     homozygote.geneSet(object, allele.names, marker, ...)

     heterozygote(object, ...)
     heterozygote.geneSet(object, allele.names, marker, ...)

     carrier(object, ...)
     carrier.geneSet(object, allele.names, marker, ...)

     dominant(object, ...)
     dominant.geneSet(object, allele.names, marker, ...)

     recessive(object, ...)
     recessive.geneSet(object, allele.names, marker, ...)

_A_r_g_u_m_e_n_t_s:

  object: 'geneSet' object 

allele.names: (optional) allele names.

  marker: (optional) marker names 

     ...: (optional) additional arguments supplied

_V_a_l_u_e:

     matrix of logicals.

_A_u_t_h_o_r(_s):

     Gregory R. Warnes warnes@bst.rochester.edu and Nitin Jain
     nitin.jain@pfizer.com

_S_e_e _A_l_s_o:

     'geneSet', 'extractAlleles'

_E_x_a_m_p_l_e_s:

     data(CAMP)
     lCAMP <- CAMP[,1:10] # 10 observations

     # see the genotypes
     genotypes(lCAMP)

     # which ones are homozygotes?
     homozygote(lCAMP)

     # which ones are carriers  for allele "2"?
     carrier(lCAMP, allele.names="2")

     # which markers are heterozygotes for marker m709
     heterozygote(lCAMP, marker="m709")

     # if '1' is dominant, which ones will show the
     # '1' phenotype for marker m47?
     dominant(lCAMP, allele.names="1", marker="m47")

     # if '2' is recessive, which ones will show the
     # '2' phenotype for marker m523?
     recessive(lCAMP, allele.names="2", marker="p523")

