hgu133aMAP              package:hgu133a              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. hgu133aMAP 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:
     January 12, 2005

     Package built Wed Jan 12 22:21:54 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(hgu133aMAP)
         # 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]]
         }

