attachInten-methods           package:xps           R Documentation

_A_t_t_a_c_h/_R_e_m_o_v_e _I_n_t_e_n_s_i_t_i_e_s

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

     Attach/remove raw CEL intensities to/from 'DataTreeSet'.

     _Usage_

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

     'removeInten(object)'

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

  object: Object of class '"DataTreeSet"'.

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

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

     When CEL files will be imported using function 'import.data', the
     raw intensities will be stored in 'ROOT' data trees. However, the
     intensities will not be saved in class 'DataTreeSet' as slot
     'data', thus avoiding memory problems. Function 'attachInten'
     allows to  fill slot 'data' on demand.

     'attachInten' exports intensities from data trees from 'ROOT' data
     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 intensities attached as
     data.frame 'data'.

     'removeInten' removes intensities from 'DataTreeSet' and replaces
     data.frame 'data' with an empty data.frame of dim(0,0).

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

     A 'DataTreeSet' object.

_N_o_t_e:

     Do not use 'attachInten' 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:

     'attachBgrd', 'removeBgrd'

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

     ## load existing 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="/"))
     dim(intensity(data.test3))

     data.test3 <- attachInten(data.test3)
     dim(intensity(data.test3))
     head(intensity(data.test3))

     data.test3 <- removeInten(data.test3)
     dim(intensity(data.test3))

