readXml            package:AffyCompatible            R Documentation

(_A_d_v_a_n_c_e_d) _R_e_a_d _X_M_L _f_i_l_e_s _o_f _A_f_f_y_m_e_t_r_i_x _s_a_m_p_l_e _a_t_t_r_i_u_b_t_e_s _o_r
_a_n_n_o_t_a_t_i_o_n

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

     This functions reads the content of Affymetrix DTT (MAGE) or ARR
     sample files, or AffxNetAffxAnnotFile array annotation files,
     return an internal representation of the underlying XML. The
     return value can be used with 'xclass' to rapidly create R objects
     representing deeply nested nodes of the document. The return value
     can also be used with 'xpathApply' in the XML package for access
     to character-based representation of the data.

_U_s_a_g_e:

     readXml(fl, ...)

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

      fl: A length-1 character vector giving the full path to the file
          to be parsed.

     ...: Additional arguments, passed to 'xmlTreeParse'.

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

     An object of class 'XMLInternalDocument'.

_A_u_t_h_o_r(_s):

     Martin Morgan

_S_e_e _A_l_s_o:

     The vignettes `Retrieving MAGE and ARR sample attributes' and
     `Annotation retrieval with NetAffxResource' for detailed
     illustration of use.

     'xclass' for instantiating objects from xpath queries.

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

     mageDir <- system.file("extdata", "DTT", package="AffyCompatible")
     mageFiles <- list.files(mageDir, full=TRUE)
     xml <- readXml(mageFiles[[1]])
     xclass(xml, "//MeasuredBioAssay")[[1]]

