Algorithms for Calculating Microarray Enrichment (ACME)

Documentation for package ‘ACME’ version 2.8.0

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.sgr	Write Affy IGB .sgr format files