cisSnpTests             package:GGtools             R Documentation

_p_e_r_f_o_r_m _t_e_s_t_s _f_o_r _e_Q_T_L _c_i_s _t_o _s_p_e_c_i_f_i_e_d _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     perform tests for eQTL cis to specified genes

_U_s_a_g_e:

     cisSnpTests(fmla, smls, radius, ...)

_A_r_g_u_m_e_n_t_s:

    fmla: standard formula. LHS can be a GeneSet with
          AnnotationIdentifier geneIdType.  RHS can be predictor
          formula component using variables in pData of 'smls' 

    smls: instance of smlSet 

  radius: numeric value: number of bases up and downstream from probe
          CHRLOC to be examined for SNP 

     ...: not in use 

_V_a_l_u_e:

     a list of cwSnpScreen instances

_N_o_t_e:

     Getting SNP locations is slow for the first event while metadata
     are brought into scope.  Subsequent calls are faster.

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     library(GSEABase)
     # two genes on chr 20
     gs1 = GeneSet(c("CPNE1", "ADA"), geneIdType = SymbolIdentifier())
     gs2 = gs1
     organism(gs2) = "Homo sapiens"
     geneIdType(gs2) = AnnotationIdentifier("illuminaHumanv1.db")
     if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
     cc = cisSnpTests(gs2~male, hmceuB36.2021, radius=1e5)
     lapply(cc, function(x) length(p.value(x@.Data[[1]])))
     cc = cisSnpTests(gs2~male, hmceuB36.2021, radius=1e6)
     lapply(cc, function(x) length(p.value(x@.Data[[1]])))

