unifilter                package:xps                R Documentation

_F_u_n_c_t_i_o_n _f_o_r _A_p_p_l_y_i_n_g _a_n _U_n_i_F_i_l_t_e_r _t_o _a_n _E_x_p_r_T_r_e_e_S_e_t

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

     This function applies an 'UniFilter' to an 'ExprTreeSet'.

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

     unifilter(xps.expr,
               filename   = character(0),
               filedir    = getwd(),
               filter     = NULL,
               minfilters = 999,
               logbase    = "log2",
               group      = character(0),
               treename   = "UniTest",
               xps.fltr   = NULL,
               xps.call   = NULL,
               update     = FALSE,
               verbose    = TRUE)

     xpsUniFilter(object, ...)

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

xps.expr: object of class 'ExprTreeSet'.

filename: file name of ROOT filter file.

 filedir: system directory where ROOT filter file should be stored.

  filter: object of class 'UniFilter'.

minfilters: minimum number of initialized filter methods to satisfy
          (default is all filters).

 logbase: convert data to logarithm of base: '"0"', '"log"', '"log2"'
          (default), '"log10"'

   group: a character vector assigning the trees of 'xps.expr' to one
          of two groups.

treename: tree name to be used in ROOT filter file.

xps.fltr: optional object of class 'FilterTreeSet'.

xps.call: optional object of class 'CallTreeSet'.

  update: logical. If 'TRUE' the existing ROOT filter file 'filename'
          will be updated.

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

  object: object of class 'ExprTreeSet'.

     ...: same arguments as function 'unifilter'.

_D_e_t_a_i_l_s:

     This function applies the different filters initialized with
     constructor 'UniFilter' to the 'ExprTreeSet' 'xps.expr'.

     Slot 'minfilters' determines the minimum number of initialized
     filters, which must be satisfied so that the mask is set to
     'flag=1'. For 'minfilters=1' at least one filter must be 
     satisfied, equivalent to logical OR; for 'minfilters=999' all
     filters must be  satisfied, equivalent to logical AND.

     If pre-filtering should be done before applying function
     'unifilter' then a 'FilterTreeSet' 'xps.fltr' must be supplied,
     created with function 'prefilter'.

     If method 'callFilter' was initialized with constructor
     'UniFilter' then 'CallTreeSet' 'xps.call' must be supplied,
     usually created with function 'mas5.call'.

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

     An 'AnalysisTreeSet'

_N_o_t_e:

     Internally, slot 'group' will be converted to integer values using
     'as.integer(as.factor(group))', thus
     'group=c("GrpA","GrpA","GrpB","GrpB")' will result in a
     fold-change of 'fc=mean(GrpB)/mean(GrpA)'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'UniFilter', 'prefilter'

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

     ## Not run: 
     ## first, load ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     ## second, create an ExprTreeSet
     data.rma <- rma(data.test3,"tmp_Test3_RMA",tmpdir="",background="pmonly",normalize=TRUE,verbose=FALSE)
     ## note: do not copy/paste this code, it is necessary only because R CMD check fails since it does not find tmp_Test3_RMA.root:
     data.rma@rootfile <- paste(.path.package("xps"),"rootdata/tmp_Test3RMA.root",sep="/")
     data.rma@filedir  <- paste(.path.package("xps"),"rootdata",sep="/")

     ## third, construct an UniFilter
     unifltr <- UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),foldchange=c(1.3,"both"),unifilter=c(0.1,"pval"))

     ## finally, create an AnalysisTreeSet
     rma.ufr <- unifilter(data.rma,"tmp_Test3Unifilter",getwd(),unifltr,group=c("GrpA","GrpA","GrpB","GrpB"),verbose=FALSE)
     str(rma.ufr)
     ## End(Not run)

