getOutliers             package:yaqcaffy             R Documentation

_G_e_t _o_u_t_l_i_e_r_s _f_o_r _t_h_e _d_i_f_f_e_r_e_n_t _Y_A_Q_C_S_t_a_t_s_O_b_j_e_c_t _s_l_o_t_s

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

     This function retrives the outliers fot the different quality
     control metrics stored in a YAQCStatsObject. Outliers are defined
     as being outside of the  mean +/- 2 stdev range or mean/2,
     mean*1.5 for the scale factor.

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

       getOutliers(YAQCStatsObject,slot)

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

YAQCStatsObject: an object of type '"YAQCStats"' 

    slot: an object of type 'string' describing the slot for which  the
          outliers should be retrieved (see details for possible  slot
          strings) 

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

     The slot strings that can be used are:

     _s_c_a_l_e _f_a_c_t_o_r "sfs"

     _a_v_e_r_a_g_e _b_a_c_k_g_r_o_u_n_d "avbg"

     _a_v_e_r_a_g_e _n_o_i_s_e "avns"

     _p_e_r_c_e_n_t_a_g_e _p_r_e_s_e_n_t "pp"

     _b_e_t_a-_a_c_t_i_n _3'/_5' _r_a_t_i_o "actin"

     _G_A_P_D_H _3'/_5' _r_a_t_i_o "gapdh"

     _i_n_t_e_r_n_a_l _b_i_o_B _c_o_n_t_r_o_l "biob"

     _i_n_t_e_r_n_a_l _b_i_o_C _c_o_n_t_r_o_l "bioc"

     _i_n_t_e_r_n_a_l _b_i_o_D _c_o_n_t_r_o_l "biod"

     _D_a_p _s_p_i_k_e _c_o_n_t_r_o_l "dap"

     _T_h_r _s_p_i_k_e _c_o_n_t_r_o_l "thr"

     _P_h_e _s_p_i_k_e _c_o_n_t_r_o_l "phe"

     _L_y_s _s_p_i_k_e _c_o_n_t_r_o_l "lys"

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

     An object of type '"numeric"' giving the outliers names and values

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

     Laurent Gatto

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

       ## load data
       library(MAQCsubsetAFX)
       data(refA)
       ## create the yaqc object
       qobj <- yaqc(refA[, 3:5])
       ## get outliers for the scale factor
       getOutliers(qobj, "sfs")

