getLocalMetaprobeIntensities package:GeneRegionScan R Documentation

_G_e_t _M_e_t_a_p_r_o_b_e _I_n_t_e_n_s_i_t_i_e_s _l_o_c_a_l_l_y

_D_e_s_c_r_i_p_t_i_o_n:

     Function that will create an expressionset from cel files.

_U_s_a_g_e:

             getLocalMetaprobeIntensities(celfilePath, analysis="rma", metaProbeSetsFile=NULL, annotation=NULL, aptProbesetSummarizePath=NULL,
             pgfPath=NULL, clfPath=NULL, cdfPath=NULL, verbose=TRUE)

_A_r_g_u_m_e_n_t_s:

celfilePath: The path to a folder that contains the cel files of
          interest.

analysis: The analysis string passed to Affymetrix Power Tools. "RMA"
          and "RMA-sketch" are recommended starting points. See APT
          documentation for complete list of possibilities.

metaProbeSetsFile: Path to a file containing meta probe set
          information. These can be downloaded from www.affymetrix.com
          and has names like HuEx\-1_0\-st\-v2.r2.dt1.hg18.full.mps.
          This choice also decides which subset of the meta probe sets
          that will be used: Core, Extended or Full.

annotation: Character string specifying which type of arrays is
          investigated.

aptProbesetSummarizePath: The path to the apt-probeset-summarize file
          from the Affymetrix Power Tools package (including the
          filename itself). You can try to leave it as NULL and see
          what happens. If you have specified the argument before it
          will be remembered.

 pgfPath: The path to a pgf file for the exon array of interest. This
          argument is mutually exclusive with the cdfPath argument.
          These files can be downloaded from www.affymetrix.com for the
          array of interest. Once given for a particular annotation,
          the location is saved for future use and can be given as NULL
          next time.

 clfPath: The path to a clf file for the exon array of interest. This
          argument is mutually exclusive with the cdfPath argument.
          These files can be downloaded from www.affymetrix.com for the
          array of interest. Once given for a particular annotation,
          the location is saved for future use and can be given as NULL
          next time.

 cdfPath: The path to a cdf file for the array of interest. This
          argument is mutually exclusive with the pgfPath and clfPath
          arguments. These files can be downloaded from
          www.affymetrix.com for the array of interest.  Once given for
          a particular annotation, the location is saved for future use
          and can be given as NULL next time.

 verbose: TRUE or FALSE.

_D_e_t_a_i_l_s:

     This function is a simple wrapper around Affymetrix Power Tools
     (APT). It is useful for importing meta probe set data from cel
     files to R environments. It will remember the location of
     annotation files, after the first use, which removes some of the
     typing otherwise included in using APT.

_V_a_l_u_e:

     An Expressionset with meta probe set values for all meta probes in
     the specified metaProbeSetFile.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'getLocalProbeIntensities', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #must correct paths and give cel files before this example will work
             listOfProbesets<-c("10321_at")
             celfilePath<-path_to_some_cel_files
             aptProbesetSummarizePath<-"~/apt/apt-cel-extract"
             cdfPath<-"~/hgu133plus2.cdf"
             getLocalMetaprobeIntensities(celfilePath, annotation="hgu133plus2", aptProbesetSummarizePath=aptProbesetSummarizePath, cdfPath=cdfPath)
             
     ## End(Not run)

