Algorithms for Calculating Microarray Enrichment (ACME)


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Documentation for package ‘ACME’ version 2.2.0

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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