indacMAP                package:indac                R Documentation

_M_a_p _b_e_t_w_e_e_n _M_a_n_u_f_a_c_t_u_r_e_r _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:

     indacMAP is an R environment that provides mappings between
     manufacturer identifiers and cytoband locations.

_D_e_t_a_i_l_s:

     Each manufacturer identifier is mapped to a vector of cytoband
     locations. The vector length may be one or longer, if there are
     multiple reported chromosomal locations for a given gene. An 'NA'
     is reported for any manufacturer identifiers that cannot be mapped
     to a cytoband at this time.

     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.   

     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:

     Entrez Gene:\<URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>. Built:
     Source data downloaded from Entrez Gene on Fri Mar 16 00:35:59
     2007

     Package built Fri Mar 16 00:42:00 2007

_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(indacMAP)
         # Remove probe identifiers 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]]
         }

