checkForDifferentAnnotation {maDB}R Documentation

Detect gene annotation differences

Description

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.

Usage

checkForDifferentAnnotation(con,chip,check.columns=c("GenBank","UniGene","LocusLink"),v=TRUE)

Arguments

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.

Details

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.

Author(s)

Johannes Rainer

References

See Also

dbConnect dbUpdateAnnotation dbGetAnnotation createDBTable

Examples






[Package maDB version 1.2.0 Index]