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: \begin{description}
     \item[scale factor] "sfs" \item[average background] "avbg"
     \item[average noise] "avns" \item[percentage present] "pp"
     \item[$beta$-actin 3'/5' ratio] "actin" \item[GAPDH 3'/5' ratio]
     "gapdh" \item[internal bioB control] "biob" \item[internal bioC
     control] "bioc" \item[internal bioD control] "biod" \item[Dap
     spike control] "dap" \item[Thr spike control] "thr" \item[Phe
     spike control] "phe" \item[Lys spike control] "lys"
     \end{description}

_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")

