ath1121501ACCNUM        package:ath1121501.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:

     'ath1121501ACCNUM' and 'ath1121501MULTIHIT' 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 'ath1121501ACCNUM' and 'ath1121501MULTIHIT' an 'NA' is
     assigned to those manufacturer IDs that can not be mapped to an
     AGI locus ID at this time.

     In addition, for 'ath1121501ACCNUM', the character string
     '"multiple"' is assigned to those manufacturer IDs that are mapped
     to more than one AGI locus ID. And for 'ath1121501MULTIHIT', 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_ATH1_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 <- ath1121501ACCNUM
       y <- ath1121501MULTIHIT
       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

