Difference between revisions of "Bsa (host object)"

Revision as of 14:57, 16 May 2013

Host object name

bsa

Class

JavaScriptBSA

Plugin

ru.biosoft.bsa (Bio-sequences analyses plugin)

JavaScript host object

ScriptableObject bsa

Site search-related analyses

Functions:

• Track MACS(Track track, Track controlTrack, String outputPath, boolean fixedLambda, int lambda1, int lambda2, int lambda3, boolean noModel, int shiftSize, int bandWidth, double genomeSize, int enrichmentRatio, int tagSize, double pValue, boolean FDR)
• void MACS14(Track track, Track controlTrack, String outputPath, Scriptable parameters)
• void compareMotifs(DataCollection sequences, DataElementPathSet siteModels, String output, Scriptable parameters)
• void createIPSModel()
• void createMatchModel()
• void createWeightMatrixModel()
• void filterOneTrackByAnother(Track inputTrack, Track filterTrack, String outputPath, Scriptable parameters)
• void geneSetSiteSearch(DataCollection yesSet, DataCollection noSet, String species, int from, int to, DataCollection profile, String outputPath, boolean optimizeCutoff, boolean optimizeWindow, double pvalueCutoff, boolean overrepresentedOnly)
• void optimizeSiteSearchAnalysis(Track inYesTrack, Track inNoTrack, String optimizationType, double pvalueCutoff, String outYesTrack, String outNoTrack, boolean overrepresentedOnly, String outSummary)
• void processTrack(Track source, String sequence, int enlargeStart, int enlargeEnd, boolean mergeOverlapping, int minimalSize, String outputPath)
• Track siteSearch(DataCollection sequences, DataCollection profile, Track intervals, String outputPath)
• TableDataCollection siteSearchSummary(Track yesTrack, Track noTrack, boolean overrepresentedOnly, String outputPath)
• void snpListToTrack(DataCollection source, String species, int fivePrimeSize, int threePrimeSize, boolean outputNonMatched, String outputPath, String annotatedTable, String genesTable, String columnName, String aggregator)