prefilter                package:xps                R Documentation

_F_u_n_c_t_i_o_n _f_o_r _A_p_p_l_y_i_n_g _a _P_r_e_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 a 'PreFilter' to an 'ExprTreeSet'.

_U_s_a_g_e:

     prefilter(xps.expr,
               filename   = character(0),
               filedir    = getwd(),
               filter     = NULL,
               minfilters = 999,
               logbase    = "log2",
               treename   = "PreFilter",
               xps.call   = NULL,
               verbose    = TRUE)

     xpsPreFilter(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 'PreFilter'.

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"'

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

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

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

  object: object of class 'ExprTreeSet'.

     ...: same arguments as function 'prefilter'.

_D_e_t_a_i_l_s:

     This function applies the different filters initialized with
     constructor 'PreFilter' 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 method 'callFilter' was initialized with constructor
     'PreFilter' then 'CallTreeSet' 'xps.call' must be supplied,
     usually created with function 'mas5.call'.

_V_a_l_u_e:

     A 'FilterTreeSet'

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'PreFilter', 'unifilter'

_E_x_a_m_p_l_e_s:

     ## 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_TestRMA",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_TestRMA.root:
     data.rma@rootfile <- paste(.path.package("xps"),"rootdata/tmp_Test3RMA.root",sep="/")
     data.rma@filedir  <- paste(.path.package("xps"),"rootdata",sep="/")

     ## third, construct a PreFilter
     prefltr <- PreFilter(mad=c(0.5,0.01),lothreshold=c(6.0,0.02,"mean"),hithreshold=c(10.5,80.0,"percent"))

     ## finally, create a FilterTreeSet
     rma.pfr <- prefilter(data.rma,"tmp_Test3Prefilter",getwd(),prefltr,2,verbose=FALSE)
     str(rma.pfr)

