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-Aug2

_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

