agMAP                   package:ag                   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:

     agMAP is an R environment that provides mappings between
     manufacturer ids and cytoband locations.

_D_e_t_a_i_l_s:

     Each manufacturer id 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 ids 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:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Tue
     May 17 18:26:20 2005

     Package built Tue May 17 18:29:49 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(agMAP)
         # 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]]
         }

