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))

