getMetaprobesetsFromRegionOfInterestpackage:GeneRegionScanR Documentation

_G_e_t _M_e_t_a _P_r_o_b_e _S_e_t _I_D_s _F_r_o_m _R_e_g_i_o_n _O_f _I_n_t_e_r_e_s_t

_D_e_s_c_r_i_p_t_i_o_n:

     Function that return the meta probe set ids located within a given
     region of the genome.

_U_s_a_g_e:

             getMetaprobesetsFromRegionOfInterest(annotation, chromosome, start, end, pythonPath=NULL, transcriptClustersFile=NULL)

_A_r_g_u_m_e_n_t_s:

annotation: A characther string giving the type of array for which
          probesets are needed. This is used to save the location of
          the transcriptClustersFile.

chromosome: The chromosome of interest. Should be given as a character
          string of the type "Chr1", "Chr2", "ChrY".

   start: A character string with the start location of interest in the
          chromosome.

     end: A character string with the end location of interest in the
          chromosome.

pythonPath: Optional character string with the path for Python
          software. This is only needed for exon arrays. If Python is
          in path this will be recognised automatically. Python can be
          downloaded from http://www.python.org.

transcriptClustersFile: The location of a transcript cluster file such
          as HuEx-1_0-st-v2.na26.hg18.transcript.csv. These can be
          downloaded from http://www.affymetrix.com.

_D_e_t_a_i_l_s:

     Since meta probe sets are only found in exon arrays, this function
     does not work with 3' IVT array files. It parses the location
     files from the http://www.affymetrix.com website using a python
     script. Admittedly this is not optional from an R-only
     point-of-view, but it works and its fast. The function will be
     updated when more R-centric ways of parsing exon array  annotation
     data is available. 

     Alternatively this data can just as well be retrieved from the
     web, but in some cases this function is faster an easier.

_V_a_l_u_e:

     A list of all probesets found in the given range on the given
     chromosome.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'getLocalProbeIntensities', 'getProbesetsFromRegionOfInterest'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #must supply transcriptClustersFile for this to work
             metaprobesets<-getMetaprobesetsFromRegionOfInterest("notusedhere", chromosome=2, start="215889955", end="216106710", transcriptClustersFile=transcriptClustersFile)
             
     ## End(Not run)

