R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
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Results 1 - 10 of 115 found.
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sdfstr2list (Package: ChemmineR) :

Returns objects of class SDFstr as list.

● Data Source: BioConductor
● Keywords: utilities
● Alias: sdfstr2list, sdfstr2list-methods, sdfstr2list<-
● 0 images

searchSim (Package: ChemmineR) :

Accepts one SDFset container and performs a >0.9 similarity PubChem fingerprint search, returning up to 200 hits in an SDFset container. The ChemMine Tools web service is used as an intermediate, to translate queries from plain HTTP POST to a PubChem Power User Gateway (PUG) query. If the input object contains multiple items, only the first is used as a query.

● Data Source: BioConductor
● Keywords: utilities
● Alias: searchSim
● 0 images

searchString (Package: ChemmineR) :

Accepts one SMILES string (Simplified Molecular Input Line Entry Specification) and performs a >0.95 similarity PubChem fingerprint search, returning the hits in an SDFset container. The ChemMine Tools web service is used as an intermediate, to translate queries from plain HTTP POST to a PubChem Power User Gateway (PUG) query.

● Data Source: BioConductor
● Keywords: utilities
● Alias: searchString
● 0 images

selectInBatches (Package: ChemmineR) :

When doing a select were the condition is a large number of ids it is not always possible to include them in a single SQL statement. This function will break the list of ids into chunks and send the query for each batch. The resutls are appended and returned as one data frame.

● Data Source: BioConductor
● Keywords:
● Alias: selectInBatches
● 0 images

setPriorities (Package: ChemmineR) :

This function should be run after loading a complete set of data. It will find each group of compounds which share the same descriptor and call the given function, priorityFn, with the compound_id numbers of the group. This function should then assign priorities to each compound-descriptor pair, however it wishes. Priorities are integer values with lower values being used in preference of higher values.

● Data Source: BioConductor
● Keywords:
● Alias: forestSizePriorities, randomPriorities, setPriorities
● 0 images

smartsSearchOB (Package: ChemmineR) :

Perform searches for SMARTS patterns using Open Babel (requires ChemmineOB package to be installed).

● Data Source: BioConductor
● Keywords:
● Alias: smartsSearchOB
● 0 images

smiles2sdf (Package: ChemmineR) :

Accepts a named vector or SMIset of SMILES (Simplified Molecular Input Line Entry Specification) strings and returns its equivalent as an SDFset container.

● Data Source: BioConductor
● Keywords: utilities
● Alias: smiles2sdf, smiles2sdfOB
● 0 images

status (Package: ChemmineR) :

Returns the status of a launched ChemMine Tools job as represented by a jobToken object.

● Data Source: BioConductor
● Keywords: utilities
● Alias: status
● 0 images

toolDetails (Package: ChemmineR) :

Connects to the ChemMine Tools web service, and provides detailed instructions and example function calls for any tool.

● Data Source: BioConductor
● Keywords: utilities
● Alias: toolDetails
● 0 images

trimNeighbors (Package: ChemmineR) :

Further reduce the cutoff value of a nearest neighbor (NN) table, as produced by nearestNeighbors. This allows one to compute a very relaxed NN table initially, and then quickly restrict it later without having to re-compute all the similarities.

● Data Source: BioConductor
● Keywords:
● Alias: trimNeighbors
● 0 images