getProbeLevelAnnotationForExonArrayspackage:GeneRegionScanR Documentation

_G_e_t _P_r_o_b_e_L_e_v_e_l _A_n_n_o_t_a_t_i_o_n _f_o_r _E_x_o_n _A_r_r_a_y_s

_D_e_s_c_r_i_p_t_i_o_n:

     Internal function that will return exon probe sequence and probe
     id for all probes in a given list of probe sets.

_U_s_a_g_e:

         getProbeLevelAnnotationForExonArrays(vectorOfProbesets, pgfPath)

_A_r_g_u_m_e_n_t_s:

vectorOfProbesets: A character string with probeset IDs.

 pgfPath: The path of a pgf file for the exon array type of interest.
          Can be downloaded from www.affymetrix.com.

_D_e_t_a_i_l_s:

     This function makes a call to readPgf in the affxparser package to
     get the sequence information. The readPgf will then load the
     entire pgf file and that might be quite memory intensive. However
     it is not possible to extract the indices of the probeset names
     without doing this. The function is primarily intended to be
     called by getLocalProbeIntensities.

     The call to readPgf sometimes gives a is.na() warning. The reason
     for this is not known, but it does not seem to affect performance.

_V_a_l_u_e:

     A dataframe with a row for each probe in the submitted probeset.
     The columns with the names "probeset_name" and "sequence" contains
     this.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'readPgf', 'getLocalProbeIntensities', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #must supply pgf file for this to work
             getProbeLevelAnnotationForExonArrays("43254543", pgfPath="~/somewhere/some.pgf")
             
     ## End(Not run)

