readMapper              package:RMAPPER              R Documentation

_q_u_e_r_y _a_n_d/_o_r _p_a_r_s_e _a _f_i_l_e _r_e_t_u_r_n_e_d _b_y _m_a_p_p_e_r._c_h_i_p._o_r_g

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

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

     readMapper(infile=NULL, mapperPW=NULL, 
       stub="http://mapper.chip.org/mapper/db-rpc?", models=NULL, ...)

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

  infile: infile - pathname to a previously generated RPC output

mapperPW: mapperPW - if query is supplied for CURL interchange, the
          credentials (in the form myname@a.b.c:mapperpw) necessary to
          permit the transaction

    stub: stub - a string giving the URL handle up to the db-rpc
          selector

  models: a vector of identifiers of MAPPER models; see their web site
          for codes

     ...: ... - all the query parameters.  see Details; 'models' will
          default to '"M1"' because the XML RPC processor fails if no
          models parameter is set.  If an unknown model parameter is
          set, then it seems to return all models.

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

     Currently (2/06) the RPC interface to MAPPER defines the following
     parameters.  You can use any of these as keywords (with bindings
     supplied using "=", e.g., 'gene="CRP"') to the 'readMapper'
     function.

     gene - you can use either GeneID or mRNA; gene name should work
     too but  it's not recommended because there often are multiple
     forms of the same  gene.

     score - the score threshold (0 by default)

     perc - the percentile (one of p50, p80, p85, p90, p95).

     eval - the E-value threshold (25 by default)

     pbases - how many basepairs to look at (default: 2000)

     pstart - what pbases is relative to (either T for transcript start
     or C  for coding sequence start - remember that in the db we have
     hits for the  region from 10,000 bp upstream of transcript start
     to 50bp after coding  sequence start)

     models - a comma-separated list of model names (to restrict the
     output  to these models only)

     sort - how to sort the results: either M (by model accession), N
     (factor  name), E (by E-value), S (by score), P (by position, the
     default)

     Thanks to Alberto Riva for this list

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

     an instance of the mapperHits class.

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

     Vince Carey <stvjc@channing.harvard.edu>

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

     mapper.chip.org

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

     readMapper(infile=system.file("txt/NM_007294.txt", package="RMAPPER"))
     if (FALSE) # you must supply your credentials to succeed over the web
      readMapper(gene="NM_007294", perc="p95", mapperPW="[usern:pwd]")

