attachCall-methods            package:xps            R Documentation

_A_t_t_a_c_h/_R_e_m_o_v_e _D_e_t_e_c_i_o_n _C_a_l_l _M_e_a_s_u_r_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Attach/remove detection call and detection p-value to/from
     'CallTreeSet'.

     _Usage_

     'attachCall(object, treenames = "*")'

     'attachPVal(object, treenames = "*")'

     'removeCall(object)'

     'removePVal(object)'

_A_r_g_u_m_e_n_t_s:

  object: Object of class '"CallTreeSet"'.

treenames: Object of class '"list"' representing the names of the 
          'ROOT' call trees.

_D_e_t_a_i_l_s:

     By default detection calls will be saved in class 'CallTreeSet' in
     slots 'data' and 'detcall', respectively, since usually the
     'data.frame's obtained as result of e.g. 'mas5.call' are of
     reasonable size. However, when computing many arrays, especially
     exon arrays at probeset levels, it may be better to compute
     detection calls with slot 'add.data=FALSE' thus avoiding memory
     problems. In this case, functions 'attachCall' and  'attachPVal'
     allow to  fill slots 'detcall' and 'data', respectively, on
     demand.

     'attachCall' exports detection calls from call trees from 'ROOT'
     call file and and saves as data.frame 'detcall'. 'treenames' is a
     vector of tree names to attach; for 'treenames="*"' all trees from
     slot 'treenames' will be exported and detection calls attached as
     data.frame 'detcall'.

     'attachPVal' exports detection p-values from call trees from
     'ROOT' call file and and saves as data.frame 'data'. 'treenames'
     is a vector of tree names to attach; for 'treenames="*"' all trees
     from slot 'treenames' will be exported and detection p-values
     attached as data.frame 'data'.

     'removeCall' removes detection calls from 'CallTreeSet' and
     replaces data.frame 'detcall' with an empty data.frame of
     dim(0,0).

     'removePVal' removes detection p-values from 'CallTreeSet' and
     replaces data.frame 'data' with an empty data.frame of dim(0,0).

_V_a_l_u_e:

     A 'CallTreeSet' object.

_N_o_t_e:

     Do not use 'attachCall' and 'attachPVal'  unless you know that
     your computer has sufficient RAM, especially when using exon
     arrays. It may be advisible to use a subset of  'treenames' only.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'attachExpr', 'removeExpr'

_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="/"))

     ## MAS5 detection call
     call.mas5 <- mas5.call(data.test3,"tmp_Test3Call0",tmpdir="",add.data=FALSE,verbose=FALSE)

     ## attach data
     call.mas5 <- attachPVal(call.mas5)
     call.mas5 <- attachCall(call.mas5)

     ## get data.frames
     pval.mas5 <- pvalData(call.mas5)
     pres.mas5 <- presCall(call.mas5)
     head(pval.mas5)
     head(pres.mas5)

     ## remove data
     call.mas5 <- removePVal(call.mas5)
     call.mas5 <- removeCall(call.mas5)

     rm(scheme.test3, data.test3)
     gc()

