find.genomic.events           package:aCGH           R Documentation

_F_i_n_d_s _t_h_e _g_e_n_o_m_i_c _e_v_e_n_t_s _a_s_s_o_c_i_a_t_e_d _w_i_t_h _e_a_c_h _o_f _t_h_e _a_r_r_a_y _C_G_H _s_a_m_p_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Finds the genomic events associated with each of the array CGH
     samples. Events include whole chromosomal gains and losses,
     aberrations, transitions, amplifications and their respective
     counts and sizes. The hmm states has to be computed before using
     this function.

_U_s_a_g_e:

     find.genomic.events(aCGH.obj, maxChrom = 23, factor = 5, maxClones = 1,
                         maxLen = 1000, absValSingle = 1, absValRegion = 1,
                         diffVal1 = 1, diffVal2 = .5, maxSize = 10000,
                         pChrom.min = .9, medChrom.min = .1)

_A_r_g_u_m_e_n_t_s:

aCGH.obj: Object of class 'aCGH'. 

maxChrom: Highest chromosomal number to find events.

  factor: Determines outliers. See 'findOutliers.func'.

maxClones: Determines aberrations. See 'findAber.func'.

  maxLen: Determines aberrations. See 'findAber.func'.

absValSingle: Determines amplifications. See 'findAmplif.func'.

absValRegion: Determines amplifications. See 'findAmplif.func'.

diffVal1: Determines amplifications. See 'findAmplif.func'.

diffVal2: Determines amplifications. See 'findAmplif.func'.

 maxSize: Determines amplifications. See 'findAmplif.func'.

pChrom.min: Determines whole chromosomal gains and losses. Chromosome
          should contain no transitions, have its absolute median equal
          or greater than 'medChrom.min' and at least 'medChrom.min'
          has to be greater or less than 0. 

medChrom.min: Determines whole chromosomal gains and losses. Chromosome
          should contain no transitions, have its absolute median equal
          or greater than 'medChrom.min' and at least 'medChrom.min'
          has to be greater or less than 0. 

_D_e_t_a_i_l_s:

     The default parameters generally work. Threshold for merging may
     be changed depending on the expected normal cell contamination
     and/or expected magnitude of the changes. AIC model generally
     works, however, may need to be readjusted depending on how liberal
     or conservative one wants to be in finding genomic events. We
     recommend BIC criterion with delta = 1 for noisier data.

_V_a_l_u_e:

num.transitions: matrix of dimensions maxChrom by number of samples. It
          contains number of transitions that were recorded on a given
          chromosome for a given sample. 

num.amplifications: matrix of dimensions maxChrom by number of samples
          It contains number of amplifications that were recorded on a
          given chromosome for a given sample. 

num.aberrations: matrix of dimensions maxChrom by number of samples. It
          contains number of focal aberrations that were recorded on a
          given chromosome for a given sample. 

num.outliers: matrix of dimensions maxChrom by number of samples.  It
          contains number of outliers that were recorded on a given
          chromosome for a given sample. 

num.transitions.binary: binary matrix of dimensions maxChrom by number
          of samples. Non-zero entry indicates whether 1 or more
          transitions were recorded on a given chromosome for a given
          sample. 

num.amplifications.binary: binary matrix of dimensions maxChrom by
          number of samples. Non-zero entry indicates whether 1 or more
          amplifications were recorded on a given chromosome for a
          given sample. 

num.aberrations.binary: binary matrix of dimensions maxChrom by number
          of samples. Non-zero entry indicates whether 1 or more focal
          aberrations were recorded on a given chromosome for a given
          sample. 

num.outliers.binary: binary matrix of dimensions maxChrom by number of
          samples. Non-zero entry indicates whether 1 or more outliers
          were recorded on a given chromosome for a given sample. 

whole.chrom.gain.loss: matrix of dimensions maxChrom by number of
          samples. Positive entry indicates that a given chromosome was
          gained in a given sample, negative entry indicates that a
          given chromosome was lost in a given sample, 0 entry is
          normal chromosome and NA marks chromosomes with one or more
          transition. 

size.amplicons: matrix of dimensions maxChrom by number of samples.
          Reports size of a given chromosome that is amplified (kb
          units) in a given sample. 

num.amplicons: matrix of dimensions maxChrom by number of samples.
          Reports number of disjoint amplicons on a given chromosome
          for a given sample. 

outliers: list containing 3 matrices of dimensions number of clones by
          number of samples. See 'findOutliers.func'. 

aberrations: list containing a matrix of dimensions number of clones by
          number of samples. See 'findAber.func'. 

transitions: list containing 2 matrices of dimensions number of clones
          by number of samples. See 'findTrans.func'. 

amplifications: list containing a matrix of dimensions number of clones
          by number of samples. See 'findAmplif.func'. 

_S_e_e _A_l_s_o:

     'aCGH' 'find.hmm.states' 'mergeFunc' 'findAber.func'
     'findTrans.func' 'findAmplif.func' 'findOutliers.func'

