agACCNUM                package:ag.db                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_s _a_n_d _A_G_I _l_o_c_u_s _I_D_s

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

     'agACCNUM' is an R object that provide mappings between
     manufacturer IDs and AGI locus IDs.

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

     Each manufacturer ID is mapped to a vector of AGI locus IDs.

     If a manufacturer ID is mapped to multiple AGI locus IDs, then all
     of these AGI locus IDs will be listed.

     For 'agACCNUM' an 'NA' is assigned to those manufacturer IDs that
     can not be mapped to an AGI locus ID at this time.

     Mappings were based on data provided by: Tair (
     ftp://ftp.arabidopsis.org/Microarrays/Affymetrix/affy_AG_array_elements-2008-5-29.txt
     ) on 2008-Aug12

_S_e_e _A_l_s_o:

     'nhit'

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

       x <- agACCNUM
       # Get the probe identifiers that are mapped to a chromosome
       mapped_probes <- mappedkeys(x)
       # Convert to a list
       xx <- as.list(x[mapped_probes])
       if(length(xx) > 0) {
         # Get the AGI locus IDs for the first five probes
         xx[1:5]
         # Get the first one
         xx[[1]]
       }

     ##   y <- agMULTIHIT
     ##  identical(keys(x), keys(y))    # TRUE

     #  nhx <- nhit(x)
     #  nhy <- nhit(y)
     #  identical(names(nhx), keys(x)) # TRUE
     #  identical(names(nhy), keys(y)) # TRUE
     #  table(nhx)
     #  table(nhy)
     #  onehit_probes <- names(nhx)[nhx != 0 & nhy == 0]
     #  x[[onehit_probes[1]]]          # a single AGI locus ID
     #  y[[onehit_probes[1]]]          # NA
     #  multihit_probes <- names(nhx)[nhy != 0]
     #  x[[multihit_probes[1]]]        # "multiple"
     #  y[[multihit_probes[1]]]        # several AGI locus IDs
     #  nohit_probes <- names(nhx)[nhx == 0]
     #  x[[nohit_probes[1]]]           # NA
     #  y[[nohit_probes[1]]]           # NA
     #  any(nhx == 0 & nhy != 0)       # FALSE
     #  ## Back to a more "normal" map (that combines the data from 'x' and 'y')
     #  xy <- as(x, "AnnDbBimap")      # 'as(y, "AnnDbBimap")' works too
     #  xy[[onehit_probes[1]]]         # a single AGI locus ID
     #  xy[[multihit_probes[1]]]       # several AGI locus IDs
     #  xy[[nohit_probes[1]]]          # NA

