org.Sc.sgdPFAM         package:org.Sc.sgd.db         R Documentation

_M_a_p _E_n_t_r_e_z _G_e_n_e _I_D_s _t_o _P_f_a_m _I_D_s

_D_e_s_c_r_i_p_t_i_o_n:

     org.Sc.sgdPFAM is an R object that provides mappings between an
     entrez gene identifier and the associated Pfam identifiers.

_D_e_t_a_i_l_s:

     Each entrez gene identifier maps to a named vector of Pfam
     identifiers.  The name for each Pfam identifier is the IPI
     accession numbe where this Pfam identifier is found.

     If the Pfam is a named NA, it means that the associated Entrez
     Gene id of this entrez gene identifier is found in an IPI entry of
     the IPI database, but there is no Pfam identifier in the entry.

     If the Pfam is a non-named NA, it means that the associated Entrez
     Gene id of this entrez gene identifier is not found in any IPI
     entry of the IPI database.

     Mappings were based on data provided by: Yeast Genome (
     ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on
     2008-Mar29

_R_e_f_e_r_e_n_c_e_s:

     Kersey P. J., Duarte J., Williams A., Karavidopoulou Y., Birney
     E., Apweiler R. The International Protein Index: An integrated
     database for proteomics experiments. Proteomics 4(7): 1985-1988
     (2004) <URL: http://www.ebi.ac.uk/IPI/IPIhelp.html>

_E_x_a_m_p_l_e_s:

             x <- org.Sc.sgdPFAM
             # Get the entrez gene identifiers that are mapped to any Pfam ID
             mapped_genes <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_genes])
             # randomly display 10 genes
             sample(xx, 10)

