R library for Bioactivity analysis

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Documentation for package ‘bioassayR’ version 1.6.1

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activeAgainst Show compounds active against a specified target
activeTargets Show targets against which a small molecule is active
addBioassayIndex Index a bioassayR database
addDataSource Add a new data source to a bioassayR database
aid Class '"bioassay"'
aid-method Class '"bioassay"'
aid<- Class '"bioassay"'
aid<--method Class '"bioassay"'
assay_type Class '"bioassay"'
assay_type-method Class '"bioassay"'
assay_type<- Class '"bioassay"'
assay_type<--method Class '"bioassay"'
bioassay Class '"bioassay"'
bioassay-class Class '"bioassay"'
BioassayDB-class Class '"BioassayDB"'
bioassaySet-class Class '"bioassaySet"'
connectBioassayDB Create a 'BioassayDB' object connected to the specified database file
disconnectBioassayDB Disconnect the database file from a 'BioassayDB' object
dropBioassay Delete an assay from a bioassayR database
dropBioassayIndex Remove index from a bioassayR database
getAssay Retrieve a bioassay
getAssays Retrieve multiple bioassays from a database
getBioassaySetByCids Create 'bioassaySet' sparse matrix object with activity data only for specified compounds
inactiveTargets Takes a single cid and returns a table of the proteins it has been found inactive against.
loadBioassay Add an assay to the database
loadIdMapping Load a target identifier mapping into a bioassayR database
newBioassayDB Create a new bioassayR database
organism Class '"bioassay"'
organism-method Class '"bioassay"'
organism<- Class '"bioassay"'
organism<--method Class '"bioassay"'
parsePubChemBioassay Parse PubChem Bioassay Data
perTargetMatrix Collapse a 'bioassaySet' object from multiple assays by combining assays with a common target
queryBioassayDB Perform a SQL query on a bioassayR database
queryBioassayDB-method Class '"BioassayDB"'
samplebioassay Sample activity data for use with bioassayR
scores Class '"bioassay"'
scores-method Class '"bioassay"'
scores<- Class '"bioassay"'
scores<--method Class '"bioassay"'
scoring Class '"bioassay"'
scoring-method Class '"bioassay"'
scoring<- Class '"bioassay"'
scoring<--method Class '"bioassay"'
screenedAtLeast Return all compounds in the database screened at least 'minTargets' times.
selectiveAgainst Identify small molecules with selective binding against a target of interest
show Class '"bioassay"'
show-method Class '"BioassayDB"'
show-method Class '"bioassay"'
show-method Class '"bioassaySet"'
source_id Class '"bioassay"'
source_id-method Class '"bioassay"'
source_id<- Class '"bioassay"'
source_id<--method Class '"bioassay"'
targets Class '"bioassay"'
targets-method Class '"bioassay"'
targets<- Class '"bioassay"'
targets<--method Class '"bioassay"'
targetSelectivity Returns the target selectivity for a specified list of compounds (cids).
target_types Class '"bioassay"'
target_types-method Class '"bioassay"'
target_types<- Class '"bioassay"'
target_types<--method Class '"bioassay"'
translateTargetId Translate a protein target GI to another identifier system