geneInfo               package:RSNPper               R Documentation

_u_s_e _C_H_I_P _S_N_P_p_e_r _X_M_L-_R_P_C _s_e_r_v_i_c_e _t_o _e_x_t_r_a_c_t _g_e_n_e _o_r _S_N_P _i_n_f_o_r_m_a_t_i_o_n

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

     SNPper is a web service at chip.org (see Riva and Kohane,
     Bioinformatics 2002). This function sets up the XML RPC call for
     the GENEINFO service.

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

     geneInfo(name=NA, acc=NA, id=NA, useOldOutput=FALSE)
     SNPinfo(dbsnpid=NA, useOldOutput=FALSE)
     geneLayout(id=NA)
     geneSNPs(id=NA, acc=NA)
     itemsInRange(item="genes", chr, start, end)
     useSNPper(cmd, parmstring)
     useSNPper2(cmd, parmstring)

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

    name: name: standard gene name

     acc: acc: mrna accession number

      id: id: SNPper gene id.  This is a 'private' nomenclature, to
          find the value for a given gene, use geneInfo.

 dbsnpid: dbsnpid: numeric value after 'rs' in dbSNP id 

    item: item: string, either "genes", "snps", or "countsnps" 

useOldOutput: logical: should the 1.5 output  format be used?  newer
          format uses an S4 object

     cmd: cmd: character string identifying an XML-RPC call honored by
          SNPPER; see list .rpcCalls in package

parmstring: parmstring: character string supplying parm=value
          information 

     chr: chr: string beginning with 'chr' identifying chromosome of
          interest

   start: start: start in base pair count of region of interest; use a
          string to avoid problems with scientific notation

     end: end: end in base pair count of region of interest; use a
          string to avoid problems with scientific notation

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

     runs an xmlEventParse on the XML-RPC response and packages the
     results.

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

     an attributed, named character vector.  The attribute gives
     version info for the SNPper database build.

_N_o_t_e:

     The itemsInRange function with item argument 'countsnps' is a hack
     that does not use XML parsing because the countsnps XML-RPC
     returns illegitimate XML tags.  Thus there is no toolInfo
     attribute for this specific call.  All other functions return
     textual information coupled with  a 'toolInfo' attribute which
     details the SNPper database version, the golden path build
     version, and the dbSNP database version from which the SNPper
     resources were constructed.

     NB: A revised version of the XML package now allows direct parsing
     of R connection streams.  This will be employed ASAP, once the
     necessary general XML infrastructure becomes prevalent.

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

     Vince Carey <stvjc@channing.harvard.edu>

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

     Riva A and Kohane IS, SNPper: retrieval and analysis of human
     SNPs, Bioinformatics 18(12) 2002, pp1681-1685.

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

     if (interactive())
      {
      print(geneInfo("CRP"))
      print(geneLayout("546"))
      tmp <- geneSNPs("546")
      print(length(tmp))
      glist <- itemsInRange("genes","chr1", "155000000", "157000000")
      print(SNPinfo("25"))
      print(length(glist))
      print(itemsInRange("countsnps","chr1", "156000000", "157000000"))
      print(useSNPper("geneinfo","&name=CRP"))
      }

