# Algorithms for Calculating Microarray Enrichment (ACME)

## Documentation for package ‘ACME’ version 2.12.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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