getGENEID          package:annotationTools          R Documentation

_F_i_n_d _g_e_n_e _I_D_s

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

     Takes a vector of probe set identifiers and an annotation table
     and retrieves the corresponding gene IDs.

_U_s_a_g_e:

     getGENEID(ps, annot, diagnose = FALSE, idCol = 19, noIDsymbol = NA, noIDprovidedSymbol = "---", sep = " /// ")

_A_r_g_u_m_e_n_t_s:

      ps: character vector containing the probe sets identifiers.

   annot: annotation table (data frame) where each row is a record and
          each column is an annotation field.

diagnose: logical. If TRUE, 3 (logical) vectors used for diagnostic
          purpose are returned in addition to the annotation. If FALSE
          (default) only the annotation is returned.

   idCol: column in annotation table containing the gene IDs.

noIDsymbol: character string to be used in output list 'geneid' if no
          gene ID is found or provided in the annotation table.

noIDprovidedSymbol: character string used in annotation table and
          indicating missing gene ID.

     sep: character string used in annotation table to separate
          multiple gene IDs.

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

     This function can be used with Affymetrix annotation files (e.g.
     'HG-U133_Plus_2_annot.csv'). It retrieves gene IDs corresponding
     to particular probe set identifiers.

     Gene IDs are returned as elements of list 'geneid'. If multiple
     gene IDs are provided for 'ps[i]' (with 'sep' separating gene IDs
     in the annotation table), a vector containing all gene IDs is
     returned as the 'i-th' element of list 'geneid'. 

     The default values for 'idCol', 'noIDsymbol', 'noIDprovidedSymbol'
     and 'sep' are chosen to suit the format of Affymetrix annotation
     files. However, options can be set to look up any annotation
     table, provided the probe set identifiers are in the first column
     and occur only once.

_V_a_l_u_e:

  geneid: list of length 'length(ps)' the 'i'-th element of which
          contains the gene ID for 'ps[i]'.

   empty: logical vector of length 'length(ps)'. 'empty[i]' is TRUE if
          'ps[i]' is empty or NA.

 noentry: logial vector of length 'length(ps)'. 'noentry[i]' is TRUE if
          'ps[i]' cannot be found in the first column of the annotation
          table.

    noid: logial vector of length 'length(ps)'. 'noid[i]' is TRUE if
          'geneid[i]==noIDprovidedSymbol' is TRUE.

_N_o_t_e:

     'getANNOTATION' provides a more flexible solution to be used with
     arbitrary annotation tables.

_A_u_t_h_o_r(_s):

     Alexandre Kuhn, alexandre.kuhn@isb-sib.ch

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

     'getANNOTATION'

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

     ##example Affymetrix annotation file and its location
     annotationFile<-'HG-U133_Plus_2_annot_part.csv'
     dataDirectory<-system.file('data',package='annotationTools')

     ##load annotation file
     annotation<-read.csv(paste(dataDirectory,annotationFile,sep='/'),colClasses='character')

     ##get gene IDs
     myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at')
     getGENEID(myPS,annotation)

     ##track origin of annotation failure for the 3 last probe set IDs
     getGENEID(myPS,annotation,diagnose=TRUE)

