homoPkgBuilder          package:AnnBuilder          R Documentation

_F_u_n_c_t_i_o_n_s _t_o _b_u_i_l_d _a _h_o_m_o_l_o_g_y _d_a_t_a _p_a_c_k_a_g_e _u_s_i_n_g _d_a_t_a _f_r_o_m _N_C_B_I

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

     This function builds a data package that maps internal HomoloGene
     ids of an organism to LocusLink ids, UniGene ids, percent identity
     of the alignment, type of similarities, and url to the source of a
     curated orthology of organisms of all pairwise best matches based
     on data from <URL: ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp>

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

     homoPkgBuilder(suffix = "homology", pkgPath, version, author, url =
     getSrcUrl("HG"))
     procHomoData(url = getSrcUrl("HG"))
     getLL2IntID(homoData, organism = "")
     mapOrgs(toMap, what = c("code","name"))
     mapPS(homoMappings, pkgName, pkgPath, tempList)
     getHomoDList(data, what = "old")
     getHomoData(entries, what = "old", objOK = FALSE)
     getOrgNameNCode()
     saveOrgNameNCode(pkgName, pkgPath, tepList)
     HomoData2List(data, what = "old")

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

  suffix: 'suffix' a character string for the suffix to be attached to
          the end of a three-letter short form for an organism to form
          the name of a package to be created for homologous genes of
          the organism

 pkgName: 'pkgName' a character string for the name of data package to
          be built

 pkgPath: 'pkgPath' a character string for the name of the directory
          where the created package will be stored

 version: 'version' a character string for the verion number of the
          package to be built

  author: 'author' a list with an author element for the name of the
          author and a maintainer element for the name and e-mail
          address of the maintainer of the package

     url: 'url' the url to the ftp site from which the source data file
          can be obtained. The default value is
          url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp}

homoData: 'homoDatgetHomoDLista' a data frame that contains the
          homology data from the source

homoMappings: 'homoMappings' same as homoData but only contains data
          for an organism of concern

organism: 'organism' a character string for the name of the organism of
          interest

   toMap: 'vect' a vector of character strings

 entries: 'entries' a vector of character strings

    data: 'data' a data matrix

    what: 'what' a character string that can either be "code" or "name"
          for function mapOrgs or "old" or "xml" for functions
          getHomoDList, getHomoData, and HomoData2List

 tepList: 'tepList' a list containing key and value pairs that are
          going to be used to replace the corresponding matching items
          in a template file for man pages

tempList: 'tempList' same as 'tepList'

   objOK: 'objOK' a boolean indicating whether the homoDATA environment
          will be a list of homoDATA (TRUE) objects or lists (FALSE)

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

     procHomoData process the source data and put the data into a data
     frame that will be used later.

     getLL2IntID maps LocusLink ids to HomoloGene internal ids

     getIntIDMapping maps HomoloGene ids to ids include LocusLink ids,
     GneBank accession numbers, percent similarity values, type of
     similarities, and the url to the curated orthology.

     mapIntID captures the reverse mapping between reciprocal
     homologous genes.

     mapOrgs converts organism codes to scientific names.

     writeRdaNMan creates an rda file and the corresponding man page
     for a data environment.

     mapPS maps HomologGene Internal ids to homoPS objects generated
     using data from the source.

     getHomoPS creates a homoPS object using data passed as a vector.

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

     procHomoData, mapIntID, and getLL2IntID returns a matrix.

     getIntIDMapping returns an R environment with mappings between
     HomoloGene internal ids and mapped data.

     getHomoPS returns a homoPS object with slots filled with data
     passed.

     mapOrgs returns a vector of character strings.

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities using R

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

     Jianhua Zhang

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     'ABPkgBuilder'

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

     # Examples are provided for only a few functions to avoid lengthy
     # execution time

