checkForDifferentAnnotation {maDB} | R Documentation |
checkForDifferentAnnotation
compares the gene annotation in the annotation
database table with the gene annotation provided by the specified R annotation package. The IDs which differ in the annotation are returned in a table.
checkForDifferentAnnotation(con,chip,check.columns=c("GenBank","UniGene","LocusLink"),v=TRUE)
con |
The connection object to the database (Connections can be opened with the dbConnect function from the RdbiPgSQL package). |
chip |
The chip for which the annotation should be checked. At the moment only Affymetrix chips are supported (eg. hgu133plus2 ). |
check.columns |
The identifiers that should be compared for the genes (Affymetrix probe sets). |
v |
if some additional informations should be written to the console. |
This function compares the annotation for the genes (or Affymetrix probe set IDs) that are available in a database table called annotation
and the corresponding R annotation package (like the hgu133plus2
package). The annotation IDs specified by the check.columns
attribute from the two different sources are compared for each gene and if they differ the gene and the different annotations are returned.
Johannes Rainer
dbConnect
dbUpdateAnnotation
dbGetAnnotation
createDBTable