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()

