heterozygosity         package:beadarraySNP         R Documentation

_F_i_n_d _r_e_g_i_o_n_s _o_f _h_o_m_o_z_y_g_o_u_s _S_N_P_s

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

     Analyze affected material without corresponding unaffected
     material in order to find regions that contain stretches of
     homozygous SNPs as an indication of loss of heterozygosity (LOH)

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

     heterozygosity(genotype, decay = 0.8, threshold = 0.1)

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

genotype: character or logical vector, genotypes of affected tissue

   decay: numeric in range (0,1)

threshold: numeric in range (0,1)

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

     The method calculates how long the stretch of homozygous SNPs is
     for each element 'delay' and 'threshold' can be set to skip
     individual heterozygous  probes in a longer stretch of homozygous
     probes. The default setting  tolerate 1 erroneous heterozygous SNP
     every 10 homozygous SNPs. Set 'threshold'  at 1 to stop discarding
     hetrozygous SNPs

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

     A numeric vector with the same length as genotype is returned.
     Higher values, of 15 and higher, indicate regions of LOH

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

     Jan Oosting

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

     'compareGenotypes', 'heterozygousSNPs'

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

       data(chr17.260)
       plot(heterozygosity(exprs(chr17.260)[,"514TV"]))

