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