annaffyCHRLOC            package:annaffy            R Documentation

_S_u_b_s_e_t _o_f _a_n_n_o_t_a_t_i_o_n _d_a_t_a _f_i_l_e _f_o_r _C_H_R_L_O_C _i_n _t_h_e _h_g_u_9_5_a_v_2 _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R environment (hash table like) object containing key
     and value pairs for the mappings between probe identifiers (key)
     and transcription startting  positions of genes on chromosomes
     (value). Keys can be accessed using ls(name of the environment)
     and values using get(key, name of the environment) or mget(keys,
     name of the environment). Values are named vectors of length 1 or
     more depending on whether a given probe id can be mapped to a
     single or multiple chromosomes. The names give the chromosome
     number of concern. NA is assigned to probe identifiers that can
     not be mapped to any chromosomal location data at this time.
     Starting positions for genes on the antisense strand have a
     leading "-" sign (e. g. -1234567). The starting positions for both
     the sense and antisense strand are number of base pairs measured
     from the p (5' end of the sense strand) to q (3' end of the sense
     strand) arms.  When a gene can not be placed on a chromosome with
     confidence, "random" is appended to the end of the name for a
     chromosomal location value. Mappings were obtained using
     refLint.txt.gz and refGene.txt.gz file from Golden Path (<URL:
     http://www.genome.ucsc.edu/goldenPath/>) from the latest release.

_D_e_t_a_i_l_s:

     Mappings were based on data provided by Human Genome Project

     Source data built: Human Genome Project built: hg16.<URL:
     http://www.genome.ucsc.edu/goldenPath/hg16/database/>. Package
     built: Wed Jan 14 22:11:01 2004 Contains 250 randomly selected
     probes

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.genome.ucsc.edu/goldenPath/hg16/database/>

_E_x_a_m_p_l_e_s:

             require("annotate") || stop("annotate unavailable")
             xx <- ls(env = annaffyCHRLOC)
             if(length(xx) > 0){
                     # Using get for value of the first key
                     get(xx[1], annaffyCHRLOC )
                     #Using mget for a few keys
                     if(length(xx) >= 3){
                             mget(xx[1:3], annaffyCHRLOC, ifnotfound=NA )
                             #Using lookUp of annotate(> 1.3.4)
                             lookUp(xx[1:3],"annaffy","CHRLOC")
                     }
             }

