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NAMESPACE
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NAMESPACE
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## IMPORTS
import(DBI, RSQLite, methods, Matrix, rjson)
importFrom("XML", xmlTreeParse, xpathSApply, xmlValue, free)
importFrom("BiocGenerics", organism, "organism<-")
importFrom("stats", "pbeta", "sd")
importClassesFrom("ChemmineR", FPset)
## EXPORTS
## S4 Classes
exportClasses(
"BioassayDB",
"bioassay",
"bioassaySet"
)
## Methods
exportMethods(
"queryBioassayDB", "show",
"aid", "source_id", "assay_type", "organism", "scoring", "targets", "target_types", "scores",
"aid<-", "source_id<-", "assay_type<-", "organism<-", "scoring<-", "targets<-", "target_types<-", "scores<-",
"activity", "sources", "source_id", "scoring",
"activity<-", "sources<-", "source_id<-", "scoring<-"
)
## Functions
export(
"connectBioassayDB",
"addDataSource",
"loadBioassay",
"dropBioassay",
"disconnectBioassayDB",
"newBioassayDB",
"addBioassayIndex",
"dropBioassayIndex",
"activeTargets",
"inactiveTargets",
"activeAgainst",
"selectiveAgainst",
"getAssay",
"getAssays",
"parsePubChemBioassay",
"getBioassaySetByCids",
"perTargetMatrix",
"targetSelectivity",
"screenedAtLeast",
"loadIdMapping",
"translateTargetId",
"assaySetTargets",
"allCids",
"allTargets",
"bioactivityFingerprint",
"scaleBioassaySet",
"crossReactivityProbability",
"crossReactivityPrior",
"trinarySimilarity"
)