ptrhomologyDATA         package:ptrhomology         R Documentation

_G_e_n_e_s _t_h_a_t _a_r_e _H_o_m_o_l_o_g_o_u_s _t_o _P_a_n _t_r_o_g_l_o_d_y_t_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This data set gives mappings between Pan troglodytes genes and
     other species based on homology. Genes that share an arbitrary
     threshold level of similarity determined by alignment of matching
     bases are termed homologous. The format is an R environment that
     maps HomoloGeneIds (which are used by NCBI to represent sequences
     of an organism) to a list of organisms that have homologous
     sequences.

_D_e_t_a_i_l_s:

     Each HomoloGeneId is mapped to a list of lists. The names of the
     outer list are the numeric code used for that organism by the
     NCBI. This is included for convenience when processing the list
     using 'lapply'.

     Each inner list consists of five named elements; homoORG,
     homoType, homoPS, homoHGID, and homoURL.

     The homoORG element indicates the organism for which there is a
     homologous gene. This will be an abbreviation of the first letter
     of the genus and the first two letters of the species. For
     instance, Homo sapiens is abbreviated _hsa_.

     The homoType element indicates the type of similarity measurement.
     This can be either _B_, indicating a reciprocal best best match
     between three or more organisms, _b_, indicating a reciprocal best
     match between two organisms, or _c_, indicating a curated homology
     relationship between two organisms.

     The homoPS element gives the percentage of identical base pair
     alignments between the homologous genes.

     The homoHGID element gives the internal HomoloGeneId.

     The homoURL element gives a url to the source for a curated
     homology.

     Note that there will not be a value for homoURL if the homoType is
     B or b, and there will not be a value for homoPS if the homoType
     is c.

     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 Mar 16 11:04:57 2007

_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(ptrhomologyDATA)

         if(length(xx) > 0){
             # Gets the homology data for the first key of ptrhomologyDATA
             homodata <- xx[[1]]
             # Gets the organism name, Entrez Gene identifier. internal HomoloGene identifier,
             # 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]
         }

