flag.summary              package:MANOR              R Documentation

_S_u_m_m_a_r_i_z_e _i_n_f_o_r_m_a_t_i_o_n _a_b_o_u_t _f_l_a_g_s _a_f_t_e_r _a_r_r_a_y _n_o_r_m_a_l_i_z_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Compute spot-level information (number of flagged spots,
     normalization parameters), and display it in a convenient way

_U_s_a_g_e:

     ## S3 method for class 'arrayCGH':
     flag.summary(arrayCGH, flag.list, flag.var="Flag", nflab="not flagged", ...)
     ## Default S3 method:
     flag.summary(spot.flags, flag.list, nflab="not flagged", ...)

_A_r_g_u_m_e_n_t_s:

arrayCGH: an object of type arrayCGH, _after normalization_ by MANOR

flag.list: a list of flags with 'flag\$char' corresponding to the
          values of 'spot.flags'

flag.var: the name of a variable of arrayCGH$arrayValues containing
          information about flags (defaults to 'Flag')

     var: the name of a variable of arrayCGH$cloneValues containing
          signal values (defaults to 'LogRatio')

spot.flags: a character vector containing information about flags

   nflab: a character vector providing a legend for "not flagged" spots

     ...: 

_D_e_t_a_i_l_s:

     This function is used by the function 'html.report' for the
     generation of an HMTL report of the normalization step. It can
     also be used by itself.

_V_a_l_u_e:

     A data.frame data.frame with 4 columns: 

    name: flag character

   label: flag label

     arg: first numeric argument of 'flag\$FUN'

   count: number of flagged spots

_N_o_t_e:

     People interested in tools for array-CGH analysis can visit our
     web-page: <URL: http://bioinfo.curie.fr>.

_A_u_t_h_o_r(_s):

     Pierre Neuvial, manor@curie.fr.

_S_e_e _A_l_s_o:

     'html.report', 'flag'

_E_x_a_m_p_l_e_s:

     data(spatial)
     data(flags)
     flag.list <- list(spatial=local.spatial.flag, spot=spot.corr.flag,
     ref.snr=ref.snr.flag, dapi.snr=dapi.snr.flag, rep=rep.flag,
     unique=unique.flag) 
     flag.list$spatial$args <- alist(var="ScaledLogRatio", by.var=NULL,
     nk=5, prop=0.25, thr=0.15, beta=1, family="symmetric") 
     flag.list$spot$args <- alist(var="SpotFlag")
     flag.list$spot$char <- "O"
     flag.list$spot$label <- "Image analysis"

     ## normalize arrayCGH
     ## Not run: 
     edge.norm <- norm.arrayCGH(edge, flag.list=flag.list,
     var="LogRatio", FUN=median, na.rm=TRUE)
     ## End(Not run) 
     fs <- flag.summary(edge.norm, flag.list=flag.list, flag.var="Flag")

     print("Flag and normalization parameters summary")
     print(fs)

