MAFfilter               package:GGBase               R Documentation

_r_e_s_t_r_i_c_t _S_N_P _i_n _a_n _s_m_l_S_e_t _t_o _r_a_n_g_e _o_f _m_i_n_o_r _a_l_l_e_l_e _f_r_e_q_u_e_n_c_i_e_s (_M_A_F)

_D_e_s_c_r_i_p_t_i_o_n:

     restrict SNP in an smlSet to range of minor allele frequencies
     (MAF)

_U_s_a_g_e:

     MAFfilter(x, lower = 0, upper = 1)

_A_r_g_u_m_e_n_t_s:

       x: smlSet instance 

   lower: numeric lower bound on minor allele frequency for keeping a
          SNP 

   upper: numeric upper bound on minor allele frequency for keeping a
          SNP 

_D_e_t_a_i_l_s:

     uses 'snp.matrix-class' summary method from snpMatrix

_V_a_l_u_e:

     revised instance of 'smlSet-class'

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     library(GGtools)
     if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
     sapply(smList(MAFfilter(hmceuB36.2021, lower=.1)), dim)

