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' and 'agMULTIHIT' are R objects 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.

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

     In addition, for 'agACCNUM', the character string '"multiple"' is
     assigned to those manufacturer IDs that are mapped to more than
     one AGI locus ID. And for 'agMULTIHIT', an 'NA' is also assigned
     to those manufacturer IDs that are mapped to a single AGI locus
     ID.

     Mappings were based on data provided by: Tair (
     ftp://ftp.arabidopsis.org/Microarrays/Affymetrix/affy_AG_array_elements-2007-5-2.txt
     ) on 2007-Oct04

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

     'nhit'

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

       x <- agACCNUM
       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

