getGENESYMBOL        package:annotationTools        R Documentation

_F_i_n_d _g_e_n_e _s_y_m_b_o_l_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 symbols.

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

     getGENESYMBOL(ps, annot, diagnose = FALSE, GScol = 15, noGSsymbol = NA, noGSprovidedSymbol = "---", 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.

   GScol: column in annotation table containing the gene IDs.

noGSsymbol: character string to be used in output list 'symbols' if no
          gene symbol is found or provided in the annotation table.

noGSprovidedSymbol: character string used in annotation table and
          indicating missing gene symbol.

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

_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 the gene symbols
     corresponding to particular probe set identifiers.

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

     The default values for 'GScol', 'noGSsymbol', 'noGSprovidedSymbol'
     and 'sep' are chosen to suit the format of Affymetrix annotation
     files. However, these 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:

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

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

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

    nogs: locial vector of length 'length(ps)'. 'nogs[i]' is TRUE if
          'symbols[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 symbols
     myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at')
     getGENESYMBOL(myPS,annotation)

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

