SAGEMapper             package:SAGElyzer             R Documentation

_A_n_n_o_t_a_t_i_n_g _S_A_G_E _t_a_g_s _u_s_i_n_g _d_a_t_a _f_r_o_m _p_u_b_l_i_c _d_a_t_a_b_a_s_e_s

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

     Functions that provide data annotation using public databases and
     package AnnBuilder

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

     SAGEMapper(tag2UG = TRUE, tagUrl =
                      "ftp://ftp.ncbi.nih.gov/pub/sage/map/Hs/NlaIII/SAGEmap_tag_ug-rel.zip",
                      organism = "Hs", fromWeb = TRUE)
     doTag2UG(fileName)
     doUG2Tag(fileName, sep = "\t", header = FALSE)
     getMapFileName()

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

  tag2UG: A boolean set to be TRUE if the mapping will be between SAGE
          tags and UniGene ids or FALSE is the mapping will be between
          UniGene ids and SAGE tags

  tagUrl: A character string for the url where mapping information can
          be downloaded

fileName: A character string for the name of the file where the mapping
          will be stored

     sep: 'sep' a character string for the separator used in the source
          file

  header: 'header' a boolean indicating whether the source file has a
          header line

organism: 'organism' a character string for the organism of concern (e.
          g. Hs for human)

 fromWeb: 'fromWeb' a boolean indicating whether the source data should
          be downloaded from the web or read from a directory locally

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

     'SAGEMapper' reads mapping data from NCBI (<URL:
     ftp://ftp.ncbi.nih.gov/pub/sage/map/Hs/NlaIII/SAGEmap_tag_ug-rel_H
     s.zip>) and produces a text file containing the mappings between
     SAGE tags and UniGene ids or UniGene ids and SAGE tags. The
     default url was valid for human genes at the time of development
     but needs to be updated when needed.

     'doTag2UG', 'doUG2Tag', and 'env2File' are called by 'SAGEMapper'
     to perfome the required functions

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

doTag2UG: Returns an R environment object containing mappings between
          SAGE tags and UniGene ids

doUG2Tag: Returns an R environment object containing mappings between
          UniGene ids SAGE tags

_N_o_t_e:

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

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

     J. Zhang

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

     The help files for package AnnBuilder provides explations on how
     to annotate data using AnnBuilder

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

     'SAGELyzer'

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

     # The following code takes a while to run and is thus inactivated
     ## Not run: 
     SAGEMapper("theMap", "", TRUE,
     "ftp://ftp.ncbi.nih.gov/pub/sage/map/Hs/NlaIII/SAGEmap_tag_ug-rel_Hs.zip")
     ## End(Not run)

