# Cross-target analysis of small molecule bioactivity

## Documentation for package ‘bioassayR’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

activeAgainst | Show compounds active against a specified target
activeTargets | Show targets against which a small molecule is active
activity | Class '"bioassaySet"'
activity-method | Class '"bioassaySet"'
activity<- | Class '"bioassaySet"'
activity<--method | Class '"bioassaySet"'
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"'
allCids | List compound cids in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object
allTargets | List distinct target(s) in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object
assaySetTargets | Return targets of assays in a 'bioassaySet' object
assay_type | Class '"bioassay"'
assay_type-method | Class '"bioassay"'
assay_type-method | Class '"bioassaySet"'
assay_type<- | Class '"bioassay"'
assay_type<--method | Class '"bioassay"'
assay_type<--method | Class '"bioassaySet"'
bioactivityFingerprint | Create an 'ChemmineR' 'FPset' object that contains bioactivity results for a given set of compounds and targets.
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
crossReactivityPrior | Compute the probability that compounds in a compound vs target matrix are promiscuous binders
crossReactivityProbability | Compute the probability that compounds in a compound vs target matrix are promiscuous binders
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-method | Class '"bioassaySet"'
organism<- | Class '"bioassay"'
organism<--method | Class '"bioassay"'
organism<--method | Class '"bioassaySet"'
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
scaleBioassaySet | Centers and standardizes the numeric activity scores for a 'bioassaySet' object (creates Z-scores)
scores | Class '"bioassay"'
scores-method | Class '"bioassay"'
scores-method | Class '"bioassaySet"'
scores<- | Class '"bioassay"'
scores<--method | Class '"bioassay"'
scores<--method | Class '"bioassaySet"'
scoring | Class '"bioassay"'
scoring-method | Class '"bioassay"'
scoring-method | Class '"bioassaySet"'
scoring<- | Class '"bioassay"'
scoring<--method | Class '"bioassay"'
scoring<--method | Class '"bioassaySet"'
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"'
sources | Class '"bioassaySet"'
sources-method | Class '"bioassaySet"'
sources<- | Class '"bioassaySet"'
sources<--method | Class '"bioassaySet"'
source_id | Class '"bioassay"'
source_id-method | Class '"bioassay"'
source_id-method | Class '"bioassaySet"'
source_id<- | Class '"bioassay"'
source_id<--method | Class '"bioassay"'
source_id<--method | Class '"bioassaySet"'
targets | Class '"bioassay"'
targets-method | Class '"bioassay"'
targets-method | Class '"bioassaySet"'
targets<- | Class '"bioassay"'
targets<--method | Class '"bioassay"'
targets<--method | Class '"bioassaySet"'
targetSelectivity | Returns the target selectivity for a specified list of compounds (cids).
target_types | Class '"bioassay"'
target_types-method | Class '"bioassay"'
target_types-method | Class '"bioassaySet"'
target_types<- | Class '"bioassay"'
target_types<--method | Class '"bioassay"'
target_types<--method | Class '"bioassaySet"'
translateTargetId | Translate a protein target identifier to another identifier system
trinarySimilarity | Computes the tanimoto similarity coefficient between the bioactivity profiles of two compounds, each represented as a column in a compound vs. target sparse matrix