hgu2beta7MAP            package:hgu2beta7            R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _p_r_o_b_e _i_d_e_n_t_i_f_i_e_r_s _a_n_d _c_y_t_o_g_e_n_e_t_i_c _m_a_p_s/_b_a_n_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     When viewed using a microscope and special stains a chromosome is
     divided into regions, or cytogenetic bands, of transverse
     alternating light and dark or fluorescent and nonfluorescent
     bands. hgu2beta7MAP maps probe identifiers to the labels of
     cytogenetic bands within chromosomes where genes represented by
     the probe ids are located

_D_e_t_a_i_l_s:

     Cytogenetic bands for most higher organisms are labeled p1, p2,
     p3, q1, q2, q3 (p and q are the p and q arms), etc., counting from
     the centromere out toward the telomeres. At higher resolutions,
     sub-bands can be seen within the bands. The sub-bands are also
     numbered from the centromere out toward the telomere. Thus, a
     label of 7q31.2 indicates that the band is on chromosome 7, q arm,
     band 3, sub-band 1, and sub-sub-band 2.   

     A given probe id may be mapped to one or more cytogenetic bands
     depending on whether genes represented by probe ids have only one
     or more chromosomal locations. Different genes may also be mapped
     to the same cytogenetic bands.

     The physical location of each band on a chromosome can be obtained
     from another environment named "organism"CYTOLOC in a separate
     data package for human(humanCHRLOC), mouse(mouseCHRLOC), and
     rat(ratCHRLOC).  

     Mappings were based on data provided by:

     LocusLink:<URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>. Built:
     February 16, 2005

     Package built Wed Feb 16 23:32:20 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.ncbi.nlm.nih.gov>

_E_x_a_m_p_l_e_s:

         # Convert the environment to a list
         xx <- as.list(hgu2beta7MAP)
         # Remove probe ids that do not map to any cytoband
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # The cytobands for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
         }

