getCompoundFeatures {ChemmineR} | R Documentation

## Get Compound Features

### Description

Get feature values for specific compounds.

### Usage

    getCompoundFeatures(conn, compoundIds, featureNames, filename = NA, keepOrder = FALSE, allowMissing = FALSE, batchSize = 1e+05)

### Arguments

`conn` | A database connection object, such as is returned by `initDb`.
`compoundIds` | A vector of compound_id numbers from this database. These are not compound names. Features will be fetched for each compound given here.
`featureNames` | A vector of features to fetch the value for, for each given compound.
`filename` | If given, dump the results into a comma seperated values (CSV) file instead of returning a data frame. This can avoid some potential memory limits when fetching large sets of data.
`keepOrder` | Ensure that the output order of values matches the order in which the compound ids where given. This will make things a little slower, so should only be used where required.
`allowMissing` | If false, raise an exception if a compound cannot be found, otherwise just silently ignore it and return data for whatever compound were found.
`batchSize` | The number of compounds to fetch in a single query. If you find your running out of memory you can try reducing this values, as well as try writing the result to a file using the `filename` parameter.

### Value

If `filename` is not given, returns a data frame with the compound_id and any given feature names. Each row represents one compound. If `filename` is given a filename then no value is returned, but the given file is created.

### Author(s)

Kevin Horan

### Examples

    	#create and initialize a new SQLite database
       conn = initDb("test1.db")

    	data(sdfsample)

    	#load data
    	ids=loadSdf(conn,sdfsample,
    			  function(sdfset)
    					data.frame(MW = MW(sdfset),  rings(sdfset,type="count",upper=6, arom=TRUE))
    			 )

    	f = getCompoundFeatures(conn,ids,c("mw","rings"))

    	unlink("test1.db")

[Package ChemmineR version 3.36.0 Index]