getANNOTATION        package:annotationTools        R Documentation

_G_e_n_e_r_a_l _a_n_n_o_t_a_t_i_o_n _f_u_n_c_t_i_o_n

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

     Takes a vector of identifiers and an annotation table and matches
     the identifiers in the table to retrieve the corresponding
     annotation. Only the first occurence of each identifier in the
     annotation table is considered.

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

     getANNOTATION(identifier, annot, diagnose = FALSE, identifierCol = 1, annotationCol = 15, noAnnotationSymbol = NA, noAnnotationProvidedSymbol = "---", sep = " /// ")

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

identifier: vector containing identifiers to be annotated.

   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.

identifierCol: column in annotation table where the provided
          identifiers are to be looked up.

annotationCol: column in annotation table containing the desired
          annotation.

noAnnotationSymbol: character string to be used in output list
          'annotation' if no annotation is found or provided.

noAnnotationProvidedSymbol: character string used in annotation table
          and indicating missing annotation.

     sep: character string used in annotation table to separate
          multiple annotation of a single identifier.

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

     The annotation is returned as elements of list 'annotation'. If a
     single annotation is given for a particular identifier, the
     corresponding element of 'annotation' has length 1. If multiple
     annotation is provided for a single identifier (i.e. character
     string with 'sep' separating multiple annotations), the mulitple
     annotation is split and the corresponding vector is returned as an
     element of list 'annotation'.

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

annotation: list of length 'length(identifier)' the 'i'-th element of
          which contains the annotation for 'identifier[i]'.

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

 noentry: locial vector of length 'length(identifier)'. 'noentry[i]' is
          TRUE if 'identifier[i]' cannot be found in
          'annot[,identifierCol]'.

noannotation: locial vector of length 'length(identifier)'.
          'noannotation[i]' is TRUE if
          'a[i]==noAnnotationProvidedSymbol' is TRUE.

_N_o_t_e:

     Use 'getMULTIANNOTATION' if the identifiers occur on more than one
     line in the annotation table.

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

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

_R_e_f_e_r_e_n_c_e_s:

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

     'getMULTIANNOTATION'

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

     ##example annotation table
     annotation<-cbind(gene=c('gene_1a, gene_1b','gene_2','gene_3','gene_4'),probe=c('probe_1','probe_2','probe_3','probe_4'),sequence=c('sequence_1','sequence_2a, sequence_2c','sequence_3',''))
     print(annotation)

     ##get sequences for probe_2, probe_3, probe_4 and probe_100
     myProbes<-c('probe_2','probe_3','probe_4','probe_100',NA)
     getANNOTATION(myProbes,annotation,identifierCol=2,annotationCol=3,noAnnotationProvidedSymbol='',sep=', ')

     ##track origin of annotation failure for the last 3 probes
     getANNOTATION(myProbes,annotation,identifierCol=2,annotationCol=3,noAnnotationProvidedSymbol='',sep=', ',diagnose=TRUE)

