readPgfEnv            package:affxparser            R Documentation

_P_a_r_s_i_n_g _a _P_G_F _f_i_l_e _u_s_i_n_g _A_f_f_y_m_e_t_r_i_x _F_u_s_i_o_n _S_D_K

_D_e_s_c_r_i_p_t_i_o_n:

     This function parses a PGF file using the Affymetrix Fusion SDK.
     PGF (probe group) files describe probes present within probe sets,
     including the type (e.g., pm, mm) of the probe and probeset.

_U_s_a_g_e:

     readPgfEnv(file, readBody = TRUE, indices = NULL)

_A_r_g_u_m_e_n_t_s:

    file: 'character(1)' providing a path to the PGF file to be input.

readBody: 'logical(1)' indicating whether the entire file should be
          parsed ('TRUE') or only the file header information
          describing the chips to which the file is releavant.

 indices: 'integer(n)' vector of positive integers indicating which
          probesets to read. These integers must be sorted (increasing)
          and unique.

_V_a_l_u_e:

     An environment. The 'header' element is always present; the
     remainder are present when 'readBody=TRUE'.

     The elements present when 'readBody=TRUE' describe probe sets,
     atoms, and probes. Elements within probe sets, for instance, are
     coordinated such that the 'i'th index of one vector (e.g.,
     'probesetId') corresponds to the 'i'th index of a second vector
     (e.g., 'probesetType'). The atoms contained within  probeset 'i'
     are in positions 'probesetStartAtom[i]:(probesetStartAtom[i+1]-1)'
     of the atom vectors. A similar map applies to probes within atoms,
     using 'atomStartProbe' as the index.

     The PGF file format includes optional elements; these elements are
     always present in the environment, but with appropriate default
     values.

  header: A list with information about the PGF file. The list contains
          elements described in the PGF file format document referenced
          below.

probesetId: integer vector of probeset identifiers.

probesetType: character vector of probeset types. Types are described
          in the PGF file format document.

probesetName: character vector of probeset names.

probesetStartAtom: integer vector of the start index (e.g., in the
          element 'atomId' of atoms belonging to this probeset).

  atomId: integer vector of atom identifiers.

atomExonPosition: integer vector of probe interrogation position
          relative to the target sequence.

atomStartProbe: integer vector of the start index (e.g., in the element
          'probeId' of probes belonging to this atom).

 probeId: integer vector of probe identifiers.

probeType: character vector of probe types. Types are described in the
          PGF file format document.

probeGcCount: integer vector of probe GC content.

probeLength: integer vector of probe lengths.

probeInterrogationPosition: integer vector of the position, within the
          probe, at which interrogation occurs.

probeSequence: character vector of the probe sequence.

_A_u_t_h_o_r(_s):

     Martin Morgan <URL: mtmorgan@fhcrc.org>

_S_e_e _A_l_s_o:

     <URL:
     https://www.affymetrix.com/support/developer/fusion/File_Format_PGF_aptv161.pdf>
     describes PGF file content.

     The internal function '.pgfProbeIndexFromProbesetIndex' provides a
     map between the indicies of probe set entries and the indicies of
     the probes contained in the probe set.

