Algorithms for Calculating Microarray Enrichment (ACME)


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Documentation for package ‘ACME’ version 2.14.0

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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-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