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)

