# Algorithms for Calculating Microarray Enrichment (ACME)

## Documentation for package ‘ACME’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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
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,aGFF-method | Class for storing GFF-like data
show,aGFFCalc-method | Class "aGFFCalc"
write.sgr | Write Affy IGB .sgr format files