aGFF-class              Class for storing GFF-like data
aGFFCalc-class          Class "aGFFCalc"
do.aGFF.calc            Perform ACME calculation
example.agff            An example ACME data structure of class aGFF
findClosestGene         Find closest refseq gene
findRegions             Find all regions in data above p-value
                        threshold
getRefflat              Get the refflat table from ucsc for the given
                        genome
read.resultsGFF         Read Nimblegen GFF files
write.sgr               Write Affy IGB .sgr format files
