attachExpr-methods            package:xps            R Documentation

_A_t_t_a_c_h/_R_e_m_o_v_e _E_x_p_r_e_s_s_i_o_n _M_e_a_s_u_r_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Attach/remove expression levels to/from 'ExprTreeSet'.

     _Usage_

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

     'removeExpr(object)'

_A_r_g_u_m_e_n_t_s:

  object: Object of class '"ExprTreeSet"'.

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

_D_e_t_a_i_l_s:

     By default expression levels will be saved in class 'ExprTreeSet'
     as slot 'data', since usually the 'data.frame' obtained as result
     of e.g. 'rma' normalization is of reasonable size. However, when
     normalizing many arrays, especially exon arrays at probeset
     levels, it may be better to compute 'rma' with slot
     'add.data=FALSE' thus avoiding memory problems. In this case,
     function 'attachExpr' allows to  fill slot 'data' on demand.

     'attachExpr' exports expression levels from expression trees from
     'ROOT' expression 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 expression levels attached as data.frame 'data'.

     'removeExpr' removes expression levels from 'ExprTreeSet' and
     replaces data.frame 'data' with an empty data.frame of dim(0,0).

_V_a_l_u_e:

     A 'ExprTreeSet' object.

_N_o_t_e:

     Do not use 'attachExpr' 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:

     'attachCall', 'removeCall'

_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="/"))

     data.rma <- rma(data.test3,"tmp_Test3RMA0",tmpdir="",background="pmonly",normalize=TRUE,add.data=FALSE,verbose=FALSE)

     ## attach data
     data.rma <- attachExpr(data.rma)

     ## get data.frame
     expr.rma <- validData(data.rma)
     head(expr.rma)

     ## remove data
     data.rma <- removeExpr(data.rma)

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

