ps2ps            package:annotationTools            R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     Takes two Affymetrix annotation files, the HomoloGene database, a
     target species ID and returns a mapping table with
     homologous/orthologous probe sets.

_U_s_a_g_e:

     ps2ps(annotation_1,annotation_2,homologene,target_species,probesets=NULL)

_A_r_g_u_m_e_n_t_s:

annotation_1: A data.frame with Affymetrix annotation for the source
          microarray format.

annotation_2: A data.frame with Affymetrix annotation for the target
          microarray format.

homologene: A data.frame with HomoloGene database.

target_species: The target species identifier (i.e. the species
          corresponding to the target microarray).

probesets: A vector of probe set identifiers. If not specified, all
          probe sets on the source microarray format are mapped
          (default).

_D_e_t_a_i_l_s:

     A table of orthologous/homologous probe sets is built by looking
     up gene IDs (corresponding to the probe sets on the source
     microarray array) in HomoloGene to find their orthologs, and
     identifying probe sets in the target microarray that probe the
     orthologous gene transcripts.

     Affymetrix annotation files can be obtained from Affymetrix
     (http://www.affymetrix.com). A flat file database version can be
     obtained from HomoloGene (http://www.ncbi.nlm.nih.gov/HomoloGene)
     Target species ID are defined by the NCBI Taxonomy database
     (http://www.ncbi.nlm.nih.gov/Taxonomy)

_V_a_l_u_e:

mappingTable: A data.frame with four columns and as many rows as there
          are probe sets in the source annotation. Eache row
          corresponds to a probe set in the source annotation
          (column1), the corresponding gene IDs (column 2), the
          orthologous gene IDs in the target species (column 3), and
          the probe sets in the target annotation correspondin to the
          orthologous gene IDs (column 4).

_A_u_t_h_o_r(_s):

     Alexandre Kuhn, alexandre.kuhn@isb-sib.ch

_E_x_a_m_p_l_e_s:

     ## Not run: 
     ##load Affymetrix annotations
     annotMouse<-read.csv('Mouse430_2_annot.csv',colClasses='character')
     annotHuman<-read.csv('HG-U133A_annot.csv',colClasses='character')

     ##load HomoloGene database
     homologene<-read.delim('homologene.data',header=FALSE)

     ##define target species ID 
     homoSapiens_ID<-9609

     ##map all probe sets on mouse array Mouse 430 2.0 to their orthologs on human array HG-U133A
     mappingTable<-ps2ps(annotMouse,annotHuman,homologene,targetSpecies)

     ##write mapping table to disk
     write.table(mappingTable,file='Mouse4302_HGU133A.txt',sep='\t',col.names=T,row.names=F,quote=FALSE)

     ##to map the first 10 probe sets given in the annotation only
     mappingTable<-ps2ps(annotMouse,annotHuman,homologene,targetSpecies,probesets=annotMouse[1:10,1])
     ## End(Not run)

