ACMECalcSet-class       Class "ACMECalcSet"
ACMESet-class           Class "ACMESet"
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 ACMESet
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
vals                    Generics defined within ACME
write.bedGraph          Write bedGraph format tracks for UCSC genome
                        browser
write.sgr               Write Affy IGB .sgr format files
