hsahomologyDATA         package:hsahomology         R Documentation

_M_a_p_s _H_o_m_o _s_a_p_i_e_n_s _H_o_m_o_l_o_G_e_n_e_I_D_s _t_o _h_o_m_o_l_o_g_y _d_a_t_a _o_f _o_t_h_e_r _o_r_g_a_n_i_s_m_s
_t_h_a_t _h_a_v_e _h_o_m_o_l_o_g_y _r_e_l_a_t_i_o_n_s_h_i_p_s _w_i_t_h _g_e_n_e_s _r_e_p_r_e_s_e_n_t_e_d _b_y _t_h_e _H_o_m_o_l_o_G_e_n_e_I_D_s

_D_e_s_c_r_i_p_t_i_o_n:

     Genes that share an arbitrary threshold level of similarity
     determined by alignment of matching bases are termed homologous.
     homologyDATA contains mappings between Homo sapiens internal 
     HomoloGeneIDs (used by NCBI to represent sequences of an organism)
     and the data concerning genes in other organisms that have been
     identified to have homology relationships with genes represented
     by the HomoloGeneIDs

_D_e_t_a_i_l_s:

     homologyDATA is an environment object with key and value pairs.
     Keys are HomoloGeneIDs and values are lists of sublists for other
     organisms that have been identified to have homology 
     relationships with the genes represented by the HomoloGeneIDs. The
     list for a given internal HomoloGeneID may have one to many
     sublists depending on whether homology relationships have been
     identified in only one or more other organisms.

     A sublist has the following elements:

     homoOrg - a named vector of a single character string whose value
     is the scientific name of the organism and name the numeric code
     used by NCBI for the organism.

     homoHGID - an integer for internal HomoloGeneID.

     homoType - a single letter for the type of similarity measurement
     between the homologous genes. homoType can be either B (reciprocal
     best best between three or more organisms), b (reciprocal best
     match between two organisms), or c (curated homology relationship
     between two organisms).

     homoPS - a percentage value measured as the percent of identity of
     base pair alignment between the homologous sequences. 

     homoURL - a url to the source if the homology relationship is a
     curated orthology.

     HomoData objects with homoType = B or b will not have any value
     for homoURL and objects with homoType = c will not have any value
     for homoPS. 

     The value of a given slot of a homoData object can be accessed by
     using homoOrg(xxx) for the homoOrg slot of the homoData object
     xxx, for example.  

     Mappings contained in homologyDATA were based on data provided by
     HomoloGene.

     HomoloGene:<URL: 
     ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp>. Built:
     HomoloGene built date not available

     Packagebuilt Fri Jan  7 09:30:30 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp>

_E_x_a_m_p_l_e_s:

         require("annotate") || stop("annotate unavailable")
         # Convert homologyDATA to a list
         xx <- as.list(hsahomologyDATA)

         if(length(xx) > 0){
             # Gets the homology data for the first key of hsahomologyDATA
             homodata <- xx[[1]]
             # Gets the organism name, LocusLink id, internal HomoloGene id,
             # GenBank accession number, type of similarity, percent
             # similarity, and URL for percent similarity for the first
             # homoData object in the list obtained previously
             homodata[[1]][["homoOrg"]]
             homodata[[1]][["homoHGID"]]
             homodata[[1]][["homoType"]]
             homodata[[1]][["homoPS"]]
             homodata[[1]][["homoURL"]]
             # Gets the values for more than one keys
             xx[1:3]
         }

