getMULTIANNOTATION {annotationTools}R Documentation

General (multiple) annotation function

Description

Takes a vector of identifiers and an annotation table and matches the identifiers in the table to retrieve the corresponding annotation. Identifiers can occur on multiple records (i.e. lines) of the annotation table.

Usage

getMULTIANNOTATION(identifier, annot, diagnose = FALSE, identifierCol = 19, annotationCol = 1, noAnnotationSymbol = NA, noAnnotationProvidedSymbol = "---")

Arguments

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 chacter 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.

Details

The annotation is returned as elements of list 'annotation'. If the 'i'-th identifier occur on multiple lines, all corresponding annotation are retrieved and output as a vector. The length of the 'i'-th element of 'annotation' thus equals the number of lines for 'identifier[i]' in the annotation table.

Value

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.

Note

getANNOTATION runs faster and is to be used if the identifiers occur only once in the annotation table.

Author(s)

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

See Also

getANNOTATION

Examples

##example annotation table
annotation<-cbind(gene=c('gene_1','gene_2','gene_2','gene_3','gene_4'),probe=c('probe_1','probe_2a','probe_2b','','probe_4'),sequence=c('sequence_1','sequence_2a','sequence_2b','','sequence_4'))
print(annotation)

##get sequences for gene_2, gene_3, gene_4 and gene_100
myGenes<-c('gene_2','gene_3','gene_4','gene_100', NA)
getMULTIANNOTATION(myGenes,annotation,identifierCol=1,annotationCol=2,noAnnotationProvidedSymbol='')

##track origin of annotation failure for the 3 last genes
getMULTIANNOTATION(myGenes,annotation,identifierCol=1,annotationCol=2,noAnnotationProvidedSymbol='',diagnose=TRUE)

[Package annotationTools version 1.12.0 Index]