Cross-target analysis of small molecule bioactivity

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Documentation for package ‘bioassayR’ version 1.37.0

• 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