GenomicReports         package:beadarraySNP         R Documentation

_G_e_n_o_m_i_c _r_e_p_o_r_t_s

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

     Create reports for all samples in a dataset.

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

     reportChromosomesSmoothCopyNumber(snpdata, grouping, normalizedTo=2, 
       smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"), 
       sample.colors = NULL, ideo.bleach=0.25, ...)
     reportSamplesSmoothCopyNumber(snpdata, grouping, normalizedTo=2, 
       smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"), 
       sample.colors=NULL, ...)
     reportGenomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, sizeSampleNames=4, 
       distance.min, upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey", 
       lohwidth=1, segment=101, orientation=c("V","H"), ...)
     reportChromosomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, distance.min,
       upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey", proportion=0.2, 
       plotLOH=TRUE, segment=101, ...)
     reportGenomeIntensityPlot(snpdata, normalizedTo=NULL, subsample=NULL, smoothing=c("mean", "quant"),
       dot.col="black", smooth.col="red", ...)

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

 snpdata: SnpSetIllumina object.

grouping: factor, elements with same value are plotted together.
          Defaults to groups of 4 in order of the samples in the
          object.

normalizedTo: numeric, a horizontal line is drawn at this position.

smooth.lambda: smoothing parameter for 'quantsmooth'.

ridge.kappa: smoothing parameter for 'quantsmooth'.

 plotLOH: indicate regions or probes with LOH, see details.

sample.colors: vector of color.

plotSampleNames: logical.

sizeSampleNames: numeric, margin size for sample names.

distance.min: numerical.

 upcolor: color.

downcolor: color.

lohcolor: color.

hetcolor: color.

lohwidth: 

 segment: integer.

orientation: ["V","H"], vertical or horizontal orientation of plot.

proportion: 

subsample: 

smoothing: Type of smoothing per chromosome.

 dot.col: color.

smooth.col: color.

ideo.bleach: numeric [0,1]

     ...: arguments are forwarded to 'plot' or 'getChangedRegions'.

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

     The first function creates plots for each group and each
     chromosome in the  dataset. The second function creates full
     genome plot for each group in the dataset. Beware that a lot of
     plots can be created, and usually you should  prepare for that, by
     redirecting the plots to 'pdf' or functions that create picture
     files like 'jpg, png, bmp'.

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

     These functions are executed for their side effects

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

     Jan Oosting

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

     'quantsmooth','prepareGenomeplot',
     'pdfChromosomesSmoothCopyNumber', 'pdfSamplesSmoothCopyNumber'

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

     data(chr17.260)
     chr17nrm <- standardNormalization(chr17.260)
     par(mfrow = c(4,2), mar = c(2,4,2,1))
     reportChromosomesSmoothCopyNumber(chr17nrm, grouping=pData(chr17.260)$Group,smooth.lambda = 4)

