flags                 package:MANOR                 R Documentation

_E_x_a_m_p_l_e_s _o_f _f_l_a_g _o_b_j_e_c_t_s _t_o _a_p_p_l_y _t_o _C_G_H _a_r_r_a_y_s

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

     This data set provides 'flag' objects that can be applied to
     'arrayCGH' objects in order to normalize them.

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

     data(flags)

_F_o_r_m_a_t:

     These 'flag' objects typically take part to a normalization
     process:

         'amplicon.flag'        flags spots with high log-ratios (temp flag)
         'chromosome.flag'      flags spots located on sexual chromosomes (named "X" and "Y")
         'control.flag'         flag control spots
         'global.spatial.flag'  corrects arrayCGH from global spatial trend on the array
         'local.spatial.flag'   flags spots belonging to local spatial bias zones on the array
         'num.chromosome.flag'  flags spots located on sexual chromosomes (named 23 and 24)
         'position.flag'        flag spots with no available genome position
         'replicate.flag'       flag spots with poor within-clone-replicate consitency
         'ref.snr.flag'         flags spots with low signal to noise ratio for reference
         'dapi.snr.flag'        flags spots with low signal to noise ratio for DAPI
         'SNR.flag'             flags spots with low signal to noise ratio
         'spot.corr.flag'       flags spots with low correlation coefficient after image analysis
         'spot.flag'            flags spots excluded by the image analysis software
         'unique.flag'          exclude last non-flagged spot of a clone
         'val.mark.flag'        flags spots corresponding to bad quality clones

_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_o_u_r_c_e:

     Institut Curie, manor@curie.fr.

_S_e_e _A_l_s_o:

     'spatial', 'norm.arrayCGH', 'flag', 'flag.summary'

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

     data(flags)

     ### complete normalization of an arrayCGH object (with spatial gradient):
     ## Initialize flag$args

     flag.list1 <- list(local.spatial=local.spatial.flag,
       global.spatial=global.spatial.flag, spot=spot.flag, SNR=SNR.flag,
       val.mark=val.mark.flag, unique=unique.flag,
       amplicon=amplicon.flag, chromosome=chromosome.flag,
       replicate=replicate.flag)

     data(spatial)
     ## Not run: 
     gradient.norm <- norm.arrayCGH(gradient, flag.list=flag.list1,
     var="LogRatio", FUN=median, na.rm=TRUE)
     ## End(Not run)
     print(gradient.norm$flags) ## spot-level flag summary (computed by flag.summary)

     ### complete normalization of an arrayCGH object (with local spatial bias):
     ## Initialize flag$args

     flag.list2 <- 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.list2$spatial$args <- alist(var="ScaledLogRatio", by.var=NULL,
     nk=5, prop=0.25, thr=0.15, beta=1, family="symmetric") 
     flag.list2$spot$args <- alist(var="SpotFlag")
     flag.list2$spot$char <- "O"
     flag.list2$spot$label <- "Image analysis"

     ## Not run: 
     edge.norm <- norm.arrayCGH(edge, flag.list=flag.list2,
     var="LogRatio", FUN=median, na.rm=TRUE)
     ## End(Not run) 
     print(edge.norm$flags) ## spot-level flag summary (computed by flag.summary)

