getProbesetsFromRegionOfInterestpackage:GeneRegionScanR Documentation

_G_e_t _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 probesets located within a given region
     of the genome.

_U_s_a_g_e:

         getProbesetsFromRegionOfInterest(annotation, chromosome, start, end, pythonPath=NULL, transcriptClustersFile=NULL, mpsToPsFile=NULL)

_A_r_g_u_m_e_n_t_s:

annotation: A characther string giving the type of array for which
          probesets are needed. Will be used to load the .db file from
          bioconductor. Optional if mps to ps and transcript cluster
          file is given.

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.

mpsToPsFile: The location of a transcript cluster file such as
          HuEx-1_0-st-v2.r2.dt1.hg18.full.mps. These can be downloaded
          from http://www.affymetrix.com. Best to use the "full" type
          file.

_D_e_t_a_i_l_s:

     While working with 3'IVT type affymetrix arrays, for which .db
     files exist within the bioconductor environment, this  function
     works in a pretty simple way. However if exon arrays are used, it
     will change to parsing the relevant library 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', 'getMetaprobesetsFromRegionOfInterest'

_E_x_a_m_p_l_e_s:

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

