haplo.scan.w          package:GeneticsBase          R Documentation

_W_r_a_p_p_e_r _f_o_r _s_e_a_r_c_h_i_n_g _f_o_r _a _t_r_a_i_t-_l_o_c_u_s _b_y _s_l_i_d_i_n_g _a _f_i_x_e_d-_w_i_d_t_h _w_i_n_d_o_w _o_v_e_r _e_a_c_h _m_a_r_k_e_r _l_o_c_u_s _a_n_d _s_c_a_n_n_i_n_g _a_l_l _p_o_s_s_i_b_l_e _h_a_p_l_o_t_y_p_e _l_e_n_g_t_h_s _w_i_t_h_i_n _t_h_e _w_i_n_d_o_w

_D_e_s_c_r_i_p_t_i_o_n:

     Wrapper for searching for a trait-locus by sliding a fixed-width
     window over each marker locus and scanning all possible haplotype
     lengths within the window.

_U_s_a_g_e:

     haplo.scan.w(geneSetObj, 
                  width = 4, 
                  miss.val = c(0, NA), 
                  em.control = haplo.em.control(), 
                  sim.control = score.sim.control())

_A_r_g_u_m_e_n_t_s:

geneSetObj: A geneSet object

   width: Width of sliding the window

miss.val: Vector of values that represent missing alleles in geno. 

em.control: A list of control parameters to determine how to perform
          the EM algorithm for estimating haplotype frequencies when
          phase is   unknown. The list is created by the function
          'haplo.em.control' - see this function for more details.

sim.control: List of control parameters to determine how simulations
          are performed for simulated p-values. The list is created by
          the function 'score.sim.control' and the default values of
          this function can be changed as desired. See
          'score.sim.control' for details. 

_D_e_t_a_i_l_s:

     Please refer to 'haplo.scan' for more details.

_V_a_l_u_e:

     A list that has class haplo.scan, which contains the following
     items:

    call: The call to haplo.scan.w 

 scan.df: A data frame containing the maximum test statistic for each
          window around each locus, and its simulated p-value. 

 max.loc: The loci (locus) which contain(s) the maximum observed test
          statistic over all haplotype lengths and all windows. 

 globalp: A p-value for the significance of the global maximum
          statistic. 

    nsim: Number of simulations performed 

_N_o_t_e:

     ~~further notes~~

_A_u_t_h_o_r(_s):

     Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus
     ross.lazarus@channing.harvard.edu

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

_S_e_e _A_l_s_o:

     'haplo.em.w', 'haplo.score.slide.w', 'haplo.score.w'

_E_x_a_m_p_l_e_s:

     ##---- Should be DIRECTLY executable !! ----
     ##-- ==>  Define data, use random,
     ##--    or do  help(data=index)  for the standard data sets.

     ## The function is currently defined as
     "haplo.scan.w"

