getMULTIANNOTATION: General (multiple) annotation function

In alexandremkuhn/annotationTools: Annotate microarrays and perform cross-species gene expression analyses using flat file databases

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

References

Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)

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)

alexandremkuhn/annotationTools documentation built on April 5, 2020, 12:59 a.m.