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]]

