plotHmmStates              package:aCGH              R Documentation

_P_l_o_t_t_i_n_g _t_h_e _e_s_t_i_m_a_t_e_d _h_m_m _s_t_a_t_e_s _a_n_d _l_o_g_2 _r_a_t_i_o_s _f_o_r _e_a_c_h _s_a_m_p_l_e.

_D_e_s_c_r_i_p_t_i_o_n:

     This function displays the estimated hmm states and log2 ratios
     for each sample.

_U_s_a_g_e:

     plotHmmStates(aCGH.obj, sample.ind, chr = 1:num.chromosomes(aCGH.obj),
                  statesres = hmm.merged(aCGH.obj), maxChrom = 23,
                  chrominfo = human.chrom.info.Jul03, yScale = c(-2, 2),
                  samplenames = sample.names(aCGH.obj))

_A_r_g_u_m_e_n_t_s:

aCGH.obj: object of class aCGH

sample.ind: index of the sample to be plotted relative to the data
          matrix (i.e. column index in the file)

statesres: matrix containing states informations. defaults to the
          states selected using the first  model selection criterionof
          'aCGH.obj'

     chr: vector of chromosomes to be plotted

  yScale: specified scale for Y-exis

maxChrom: highest chromosome to show

chrominfo: a chromosomal information associated with the mapping of the
          data

samplenames: vector of sample names

_D_e_t_a_i_l_s:

     Each chromosome is plotted on a separate  page and contains two
     figures. The top figure shows the observed log2ratios and the
     bottom figure shows predicted values for all clones but outliers
     which show observed values. The genomic events are indicated on
     both figures as following. The first clone after transition is
     indicated with solid blue line and the last clone after
     transitions is shown with dotted green line. Focal aberrations
     clones are colored orange, amplifications are colored red and
     outliers are yellow.

_A_u_t_h_o_r(_s):

     Jane Fridlyand

_R_e_f_e_r_e_n_c_e_s:

     Application of Hidden Markov Models to the analysis of the array
     CGH data, Fridlyand et.al., _JMVA_, 2004

_S_e_e _A_l_s_o:

     'aCGH' 'find.hmm.states' 'plotGenome'

_E_x_a_m_p_l_e_s:

     data(colorectal)
     plotHmmStates(colorectal, 1)

