html.report              package:MANOR              R Documentation

_G_e_n_e_r_a_t_e _a_n _H_T_M_L _r_e_p_o_r_t _o_f _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:

     Create an HTML file with various illustrations of array
     normalization, including plots before and after normalization, and
     statistics about flagged spots and clones

_U_s_a_g_e:

       ## S3 method for class 'arrayCGH':
       html.report(array.norm, array.nonorm=NULL, dir.out=".",
     array.name=NULL, x="PosOrder", y=c("LogRatioNorm", "LogRatio"), chrLim=NULL,
     ylim=NULL, zlim=NULL, clim=NULL, intensity=NULL, light=FALSE, file.name="report",
     width=10, height=5, ...) 
       ## Default S3 method:
       html.report(spot.data, clone.data=NULL, flag.data=NULL, quality.data=NULL, ...)

_A_r_g_u_m_e_n_t_s:

array.norm: an object of type 'arrayCGH' after normalization step

array.nonorm: an optional object of type arrayCGH after a normalization
          step with no flags

spot.data: a data.frame containing spot-level informations (e.g.
          'arrayCGH\$arrayValues')

clone.data: a data.frame containing clone-level informations (e.g.
          'arrayCGH\$cloneValues')

flag.data: a data.frame containing information about flags, with fields
          'char', 'label', 'arg', 'count' as generated by function
          'flag.summary'

quality.data: a data.frame containing information about quality scores
          with fields 'name', 'label', 'score' as generated by function
          'qscore.summary'

 dir.out: absolute path of a directory where the file is generated
          (defaults to the current directory)

array.name: name or identifier of the array

       x: a variable name from 'arrayCGH\$cloneValues' giving the order
          position of the clones along the genome (defaults to
          'PosOrder')

       y: a vector of one or two variable names to be passed to
          'report.plot'

  chrLim: an optional variable name from 'arrayCGH\$cloneValues' giving
          the limits of each chromosome

    ylim: a numeric vector of length 2 to be passed to 'report.plot': y
          axis range of the genomic profile display

    clim: a numeric vector of length 2 to be passed to 'report.plot':
          color range of the genomic profile

    zlim: a numeric vector of length 2 to be passed to 'report.plot':
          color range for array image display

intensity: an optional list with names c("M.var", "A.var", "pred.var",
          "span"). The first 3 items specify existing variable names
          from 'arrayCGH\$arrayValues' that will be used to draw a
          MA-plot. The last item is the value of the loess 'span'

   light: boolean value: if (light), only the core of the html file is
          generated; if (!light), a complete html file is generated

file.name: file name of the generated report (defaults to "report")

   width: plot width, in inches

  height: plot height, in inches

     ...: further arguments to be passed to 'report.plot'

_D_e_t_a_i_l_s:

     This function creates an HTML report file showing - the array
     image and the genome representation before normalization (if
     'array.nonorm' is provided) and after normalization, and
     optionally a MA-plot - a table with information about the number
     of flagged spots for each flag, and the number of remaining spots
     after normalization - a table with information about various
     quality criteria for the array

_V_a_l_u_e:

     none

_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:

     'flag.summary', 'report.plot'

