gwSnpTests              package:GGtools              R Documentation

_m_e_t_h_o_d_s _f_o_r _i_t_e_r_a_t_i_n_g _a_s_s_o_c_i_a_t_i_o_n _t_e_s_t_s (_e_x_p_r_e_s_s_i_o_n _v_s _S_N_P)
_a_c_r_o_s_s _g_e_n_o_m_e_s _o_r _c_h_r_o_m_o_s_o_m_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     methods for iterating association tests (expression vs SNP) across
     genomes or chromosomes

_U_s_a_g_e:

     gwSnpTests(sym, sms, cnum, ...)

_A_r_g_u_m_e_n_t_s:

     sym: genesym, probeId, or formula instance

     sms: smlSet instance

    cnum: chrnum instance or missing

     ...: ...

_D_e_t_a_i_l_s:

     invokes snpMatrix test procedures as appropriate

     gwSnpScreen is deprecated and simply throws a message indicating
     this.

_V_a_l_u_e:

     gwSnpScreenResult or cwSnpScreenResult instance

_A_u_t_h_o_r(_s):

     Vince Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
     # condense to founders only
     hmFou = hmceuB36.2021[, which(hmceuB36.2021$isFounder)]
     # show basic formula fit
     f1 = gwSnpTests(genesym("CPNE1")~male, hmFou, chrnum(20))
     f1
     plot(f1)
     # show how to avoid adjusted fit
     f1b = gwSnpTests(genesym("CPNE1")~1-1, hmFou, chrnum(20))
     # show gene set modeling on chromosome
     library(GSEABase)
     gs1 = GeneSet(c("CPNE1", "ADA"))
     geneIdType(gs1) = SymbolIdentifier()
     f2 = gwSnpTests(gs1~male, hmFou, chrnum(20))
     f2
     names(f2)
     plot(f2[["ADA"]])
     # show 'smlSet-wide' fit
     f3 = gwSnpTests(gs1~male, hmFou)
     f3

