| ACMECalcSet-class | Class "ACMECalcSet" |
| ACMESet-class | Class "ACMESet" |
| aGFF-class | Class for storing GFF-like data |
| aGFFCalc-class | Class "aGFFCalc" |
| chromosome | Generics defined within ACME |
| chromosome-method | Class "ACMESet" |
| cutpoints | Generics defined within ACME |
| cutpoints-method | Class "ACMECalcSet" |
| do.aGFF.calc | Perform ACME calculation |
| end | Generics defined within ACME |
| end-method | Class "ACMESet" |
| 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 |
| plot | Generics defined within ACME |
| plot-method | Class "ACMECalcSet" |
| plot-method | Class "ACMESet" |
| plot-method | Class for storing GFF-like data |
| plot-method | Class "aGFFCalc" |
| print-method | Class for storing GFF-like data |
| print-method | Class "aGFFCalc" |
| read.resultsGFF | Read Nimblegen GFF files |
| show-method | Class "ACMECalcSet" |
| show-method | Class for storing GFF-like data |
| show-method | Class "aGFFCalc" |
| start | Generics defined within ACME |
| start-method | Class "ACMESet" |
| threshold | Generics defined within ACME |
| threshold-method | Class "ACMECalcSet" |
| vals | Generics defined within ACME |
| vals-method | Class "ACMECalcSet" |
| write.bedGraph | Write bedGraph format tracks for UCSC genome browser |
| write.sgr | Write Affy IGB .sgr format files |