compareGenotypes        package:beadarraySNP        R Documentation

_C_o_m_p_a_r_e _g_e_n_o_t_y_p_e_s

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

     Pairwise comparison of genotypes between unaffected and affected
     tissue from the same subject

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

     compareGenotypes(genotypeT, genotypeN)

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

genotypeT: character or logical vector, genotypes of affected tissue

genotypeN: character or logical vector with same length as genotypeT,
          genotypes of  unaffected, normal tissue

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

     Heterozygous probes have one the following values. 'TRUE', ''H''
     or ''AB''.  All other values are considered homozygous. The
     primary purpose of the method  is to find probes with loss of
     heterozygosity (LOH), where the unaffected probe  is heterozygous
     and the affected is called homozygous.

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

     A vector with the same length as the arguments where each element
     can have one of four values 

     'u': Uninformative: both affected and normal are homozygous

     'i': Informative: both affected and unaffected heterozygous

     'l': Loss: unaffected heterozygous, affected homozygous

     'a': Artefact: unaffected homozygous, affected heterozygous

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

     Jan Oosting

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

     'heterozygousSNPs'

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

     data(chr17.260)
     compareGenotypes(exprs(chr17.260)[,"514TV"],exprs(chr17.260)[,"514NP"])

