buildSNPannotation         package:siggenes         R Documentation

_C_o_n_s_t_r_u_c_t _A_n_n_o_t_a_t_i_o_n _f_o_r _A_f_f_y_m_e_t_r_i_x _S_N_P _C_h_i_p_s

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

     Constructs a data frame from a metadata package containing
     annotations for the SNPs from the corresponding Affymetrix SNP
     Chip

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

       buildSNPannotation(pkg, rs = TRUE, allele = TRUE, gene = TRUE,
         chromosome = FALSE, position = FALSE, strand = FALSE, cytoband = FALSE, 
         max.genes = 0, lib.loc = NULL, others = NULL, subset = NULL, 
         pattern = NULL, na.rm = TRUE)

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

     pkg: the name of the metadata package from which the data frame
          containing the annotations of the SNPs should be generated

      rs: should the RefSNP-ID of the SNPs be added to the data frame?

  allele: should the two alleles of each SNP be added to the data
          frame?

    gene: should the genes associated with the SNPs be added to the
          data frame?

chromosome: should the chromosome to which the respective SNP belongs
          be added to the data frame?

position: should the physical positions of the SNPs be added to the
          data frame?

  strand: should the strands be added to the data frame?

cytoband: logical indicating whether the cytoband of each SNP is added
          to the data frame

max.genes: integer specifying the maximum number of genes associated
          with the respective SNP that should be stored in the data
          frame. By default, all entries are considered. The
          corresponding column of the data frame can also be shortened
          afterwards using 'shortenGeneDescription'. Shortened entries
          are marked by '...' at the end of the entries

 lib.loc: the directory in which the metadata package is stored. Needs
          only to be specified if it is not stored in the usual
          directory of the packages

  others: character string or vector naming other entries of the object
          'featureSet' saved in 'pkg' that should be added to the data
          frame

  subset: character string consisting of the probe set IDs of the SNPs
          for which the data frame should be generated. The data frame
          will contain all SNPs if 'subset = NULL'

 pattern: character string specifying the pattern of the probe set IDs
          of the SNPs for which the data frame should be generated. For
          example, 'pattern = "SNP%"' will lead to a data frame
          containing all SNPs whose probe set ID start with "SNP"

   na.rm: should the rows of the data frame corresponding to SNPs
          specified by 'subset' for which no information is available
          in the metadata package be removed?

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

     a data frame composed of annotations for the SNPs for which
     information is available in the specified metadata package

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

     Holger Schwender, holger.schw@gmx.de

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

     'shortenGeneDescription', 'link.genes', 'link.siggenes',
     'sam2html'

