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

_O_R_F _I_D_s _t_o _C_h_r_o_m_o_s_o_m_a_l _L_o_c_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     org.Sc.sgdCHRLOC is an R object that maps ORF identifiers to the
     starting position of the gene. The position of a gene is measured
     as the number of base pairs.

     The CHRLOCEND mapping is the same as the CHRLOC mapping except
     that it specifies the ending base of a gene instead of the start.

_D_e_t_a_i_l_s:

     Each ORF identifier maps to a named vector of chromosomal
     locations, where the name indicates the chromosome. 

     Chromosomal locations on both the sense and antisense strands are
     measured as the number of base pairs from the p (5' end of the
     sense strand) to q (3' end of the sense strand) arms. Chromosomal
     locations on the antisense strand have a leading "-" sign (e. g.
     -1234567). 

     Since some genes have multiple start sites, this field can map to
     multiple locations.

     Mappings were based on data provided by: Yeast Genome (
     ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on
     2008-Sep06

_E_x_a_m_p_l_e_s:

             x <- org.Sc.sgdCHRLOC
             # Get the ORF identifiers that are mapped to chromosome locations
             mapped_genes <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_genes])
             if(length(xx) > 0) {
               # Get the CHRLOC for the first five genes
               xx[1:5]
               # Get the first one
               xx[[1]]
             }

