dropBioassay: Delete an assay from a bioassayR database

In bioassayR: Cross-target analysis of small molecule bioactivity

Description

Allows the user to delete all records from the database associated with a given assay identifier.

Usage

dropBioassay(database, aid)

Arguments

database	A BioassayDB database to remove an assay from.
aid	The assay identifier string (aid), matching an aid for an assay loaded into the database.

Author(s)

Tyler Backman

Examples

## create sample database and load with data
myDatabaseFilename <- tempfile()
mydb <- newBioassayDB(myDatabaseFilename, indexed=FALSE)
extdata_dir <- system.file("extdata", package="bioassayR")
assayDescriptionFile <- file.path(extdata_dir, "exampleAssay.xml")
activityScoresFile <- file.path(extdata_dir, "exampleScores.csv")
myAssay <- parsePubChemBioassay("1000", activityScoresFile, assayDescriptionFile)
addDataSource(mydb, description="PubChem BioAssay", version="unknown")
loadBioassay(mydb, myAssay)

## delete the loaded assay
dropBioassay(mydb, "1000")

## disconnect from and delete sample database
disconnectBioassayDB(mydb)
unlink(myDatabaseFilename)

Example output

Loading required package: DBI
Loading required package: RSQLite
Loading required package: Matrix
Loading required package: rjson
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'bioassayR'

The following objects are masked from 'package:BiocGenerics':

    organism, organism<-

Warning messages:
1: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
2: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
3: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
4: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
5: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning messages:
1: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data). 
2: Factors converted to character 
3: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning messages:
1: Factors converted to character 
2: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
3: Factors converted to character 
4: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
5: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning messages:
1: Factors converted to character 
2: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
3: Factors converted to character 
4: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
5: Factors converted to character 
6: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries

bioassayR documentation built on March 1, 2021, 2 a.m.