cdfenvs              package:altcdfenvs              R Documentation

_f_u_n_c_t_i_o_n_s _r_e_l_a_t_e_d _t_o _c_d_f_e_n_v_s

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

     A set of functions to handle cdfenvs

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

     wrapCdfEnvAffy(cdfenv, nrow.chip, ncol.chip, chiptype, check = TRUE,
                    verbose = FALSE)
     getCdfEnvAffy(abatch)
     buildCdfEnv.matchprobes(matches, ids, probes.pack, abatch=NULL,
                             nrow.chip=NULL, ncol.chip=NULL, chiptype=NULL,
                             mm=NA, simplify = TRUE,
                             x.colname = "x", y.colname = "y", verbose=FALSE)

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

  abatch: an 'AffyBatch'

  cdfenv: A cdfenv environment

   check: perform consistency check or not

chiptype: A name for the chip type

     ids: a vector of probe set identifiers for the matches

 matches: a list as returned by the function 'matchprobes'

      mm: The value to store for MMs

ncol.chip: The number of columns for the chip type

nrow.chip: The number of rows for the chip type

probes.pack: The name of the probe package

simplify: Simplify the environment created by removing the ids without
          any matching probe

x.colname, y.colname: see the 'getxy.probeseq'

 verbose: verbosity ('TRUE' or 'FALSE')

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

     An instance of class 'CdfEnvAffy'.

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

     ## See the main vignette

