export.filter              package:xps              R Documentation

_E_x_p_o_r_t _f_i_l_t_e_r _d_a_t_a _a_s _t_e_x_t _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Export data from classes 'FilterTreeSet' or 'AnalysisTreeSet' to
     'outfile'.

_U_s_a_g_e:

     export.filter(xps.fltr, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

xps.fltr: an object of type 'FilterTreeSet' or 'AnalysisTreeSet'.

treename: tree name to export.

treetype: type of tree(s) to export, 'pfr', 'ufr' or 'stt'.

 varlist: names of tree leaves to export.

 outfile: name of output file.

     sep: column separator

as.dataframe: if 'TRUE' a data.frame will be returned.

 verbose: logical, if 'TRUE' print status information.

_D_e_t_a_i_l_s:

     Export data from classes 'FilterTreeSet', or 'AnalysisTreeSet' to
     'outfile'.

     Parameter 'varlist' lists the parameters to export: 
      - parameters are separated by ":", e.g.
     'varlist="fUnitName:fFlag"'. 
      - for 'varlist="*"' all valid parameters will be exported.

     For class 'FilterTreeSet' the following 'varlist' parameters are
     valid:

         'fUnitName':  unit name (probeset ID).
         'fFlag':      mask.

     For class 'AnalysisTreeSet' 'varlist' can contain annotation
     parameters and parameters of the resulting data. 
      Following 'varlist' annotation parameters are valid:

         'fUnitName':      unit name (probeset ID).
         'fTranscriptID':  transcript_id (probeset ID).
         'fName':          gene name.
         'fSymbol':        gene symbol.
         'fAccession':     mRNA accession such as Refseq ID.
         'fEntrezID':      entrez ID.
         'fChromosome':    chromosome.
         'fStart':         start position.
         'fStop':          stop position.
         'fStrand':        strand on chromosome.
         'fCytoBand':      cytoband.

     For class 'AnalysisTreeSet' the following 'varlist' parameters are
     valid:

         'mn1':   mean of group 1.
         'mn2':   mean of group 2.
         'fc':    fold-change fc=mn2/mn1.
         'se':    standard error.
         'df':    degree of freedom.
         'stat':  t-statistic.
         'pval':  p-value.
         'nper':  number of permutations.
         'pcha':  p-chance.
         'padj':  adjusted p-value.
         'flag':  flag.
         'mask':  only rows with 'flag=1' will be exported.

_V_a_l_u_e:

     If 'as.dataframe' is 'TRUE', the data will be imported into the
     current R session as 'data.frame'. Otherwise, 'NULL' will be
     returned.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'export-methods'

