getMULTIANNOTATION: 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.

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.

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.

Examples

Run this code

##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)