metaProbesets              package:xps              R Documentation

_C_r_e_a_t_e _M_e_t_a_P_r_o_b_e_s_e_t _F_i_l_e _f_o_r _A_P_T

_D_e_s_c_r_i_p_t_i_o_n:

     Create MetaProbeset File for APT function
     "apt-probeset-summarize".

_U_s_a_g_e:

     metaProbesets(xps.scheme, infile = character(0), outfile = character(0), exonlevel="metacore")

_A_r_g_u_m_e_n_t_s:

xps.scheme: exon 'SchemeTreeSet'.

  infile: Name of file containing exon transcript_cluster_ids.

 outfile: Name of resulting file containing meta probeset definitions.

exonlevel: exon annotation level determining which probes should be
          used.

_D_e_t_a_i_l_s:

     This function allows to create a metaprobeset file for APT
     function "apt-probeset-summarize" to be used with option "-m". The
     'infile' must contain exon transcript_cluster_ids, one per line,
     e.g. one can export the 'rownames(data.rma)' 
      The resulting file may be useful if you want to compare results
     created with 'xps' to results created with APT function
     "apt-probeset-summarize".

_V_a_l_u_e:

     None.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_E_x_a_m_p_l_e_s:

     ## Not run: 
     ## first, load ROOT exon scheme file:
     scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
     scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na25.root",sep="/"))

     metaProbesets(scheme.exon,"metacore.txt","metacoreList.mps","metacore")
     ## End(Not run)

