unifyMappings           package:AnnBuilder           R Documentation

_A _f_u_n_c_t_i_o_n _t_o _u_n_i_f_y _m_a_p_p_i_n_g _r_e_s_u_l_t _f_r_o_m _d_i_f_f_e_r_e_n_t _s_o_u_r_c_e_s

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

     Given a base file and mappings from different sources, this
     function resolves the differences among sources in mapping results
     using a voting sheme and derives unified mapping results for
     targets in the base file

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

     unifyMappings(base, ll, ug, otherSrc, fromWeb)

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

    base: 'base' a matrix with two columns. The first column contains
          the target items (genes) to be mapped and the second the know
          mappings of the target to GenBank accession numbers or
          UniGene ids

      ll: 'll' an object of class LL

      ug: 'ug' an object of class UG

otherSrc: 'otherSrc' a vector of character strings for names of files
          that also contain mappings of the target genes in base. The
          files are assumed to have two columns with the first one
          being target genes and second one being the desired mappings

 fromWeb: 'fromWeb' a boolean to indicate whether the source data will
          be read from the web or a local file

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

     ll and ug have methods to parse the data from LocusLink and
     UniGene to obtain desored mappings to target genes in base.
     Correct source urls and parsers are needed to obtain the desired
     mappings

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

     The function returns a matrix with four columns. The first two are
     the same as the columns of base, the third are unified mappings,
     and forth are statistics of the agreement among sources.

_N_o_t_e:

     This function is part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang

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

     'LL', 'UG'

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

     myDir <- file.path(.path.package("AnnBuilder"), "temp")
     geneNMap <- matrix(c("32468_f_at", "D90278", "32469_at", "L00693",
                        "32481_at", "AL031663", "33825_at", " X68733",
                        "35730_at", "X03350", "36512_at", "L32179",
                        "38912_at", "D90042", "38936_at", "M16652",
                        "39368_at", "AL031668"), ncol = 2, byrow = TRUE)
     colnames(geneNMap) <- c("PROBE", "ACCNUM")
     write.table(geneNMap, file = file.path(myDir, "geneNMap"), sep = "\t",
     quote = FALSE, row.names = FALSE, col.names = FALSE)

     temp <- matrix(c("32468_f_at", NA, "32469_at", "2",
                        "32481_at", NA, "33825_at", " 9",
                        "35730_at", "1576", "36512_at", NA,
                        "38912_at", "10", "38936_at", NA,
                        "39368_at", NA), ncol = 2, byrow = TRUE)
     temp
     write.table(temp, file = file.path(myDir, "srcone"), sep = "\t",
     quote = FALSE, row.names = FALSE, col.names = FALSE)
     temp <- matrix(c("32468_f_at", NA, "32469_at", NA,
                        "32481_at", "7051", "33825_at", NA,
                        "35730_at", NA, "36512_at", "1084",
                        "38912_at", NA, "38936_at", NA,
                        "39368_at", "89"), ncol = 2, byrow = TRUE)
     temp
     write.table(temp, file = file.path(myDir, "srctwo"), sep = "\t",
     quote = FALSE, row.names = FALSE, col.names = FALSE)
     otherMapping <- c(srcone = file.path(myDir, "srcone"),
     srctwo = file.path(myDir, "srctwo"))

     baseFile <-  file.path(myDir, "geneNMap")
     llParser <- file.path(.path.package("AnnBuilder"), "data", "gbLLParser")
     ugParser <- file.path(.path.package("AnnBuilder"), "data", "gbUGParser")
     if(.Platform$OS.type == "unix"){
         llUrl <-  "http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz"
         ugUrl <-  "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz"
         fromWeb = TRUE
     }else{
         llUrl <- file.path(.path.package("AnnBuilder"), "data", "Tll_tmpl")
         ugUrl <- file.path(.path.package("AnnBuilder"), "data", "Ths.data")
         fromWeb = FALSE
     }
     ll <- LL(srcUrl = llUrl, parser = llParser, baseFile = baseFile)
     ug <- UG(srcUrl = ugUrl, parser = ugParser, baseFile = baseFile,
     organism = "human") 
     # Only works interactively
     if(interactive()){
         unified <- unifyMappings(base =  geneNMap, ll = ll, ug = ug,
                    otherSrc = otherMapping, fromWeb = fromWeb)
         read.table(unified, sep = "\t", header = FALSE)

         unlink(c(file.path(myDir, "geneNMap"), file.path(myDir, "srcone"),
         file.path(myDir, "srctwo"), unified))
     }

