CNA                 package:DNAcopy                 R Documentation

_C_r_e_a_t_e '_C_o_p_y _N_u_m_b_e_r _A_r_r_a_y' _d_a_t_a _o_b_j_e_c_t

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

     Creates a `copy number array' data object used for DNA copy number
     analyses by programs such as circular binary segmentation (CBS).

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

       CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
                      sampleid=NULL)

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

genomdat: a vector or matrix of data from array-CGH, ROMA, or other
          copy number experiments. If it is a matrix the rows
          correspond to the markers and the columns to the samples.

   chrom: the chromosomes (or other group identifier) from which the
          markers came.  Vector of length same as the number of rows of
          genomdat.  If one wants the chromosomes to be ordered in the
          natural order, this variable should be numeric or ordered
          category.

  maploc: the locations of marker on the genome.  Vector of length same
          as the number of rows of genomdat. This has to be numeric.

data.type: logratio (aCGH, ROMA, etc.) or binary (LOH).

sampleid: sample identifier.  If missing the samples are named by
          prefixing "Sample" to consecutive integers.

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

     An object of class 'CNA'.  There is a 'print' method that gives
     the number of samples and probes and the type of data.

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

     data(coriell)

     #Combine into one CNA object to prepare for analysis on Chromosomes 1-23

     CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
                       coriell$Chromosome,coriell$Position,
                       data.type="logratio",sampleid=c("c05296","c13330"))

