getPcCand.ExactMass: Retrieve CID Count or CID list by Exact Mass from PubChem

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

Retrieves a count of CIDs or CID list from PubChem using entrez/eUtils . Default behaviour is to retrieve CID count only, or a short CID list in ascending order. RMassBank is used to calculate the ppm range. Thanks to Paul Thiessen and Evan Bolton from PubChem team for assistance.

Usage

getPcCand.ExactMass(ExactMass, ppm=5, CountOnly=TRUE, RetMax=20, sortAsc=TRUE, timeout=10)

Arguments

ExactMass	Exact mass to search
ppm	Mass error (ppm, not Da) to search. Default 5, adds to both sides of ExactMass.
CountOnly	Default TRUE returns a count of the CIDs, FALSE returns a list of CIDs of length RetMax.
RetMax	Number of CIDs to return. Default 20 is the eUtils default. For large queries this needs to be set much larger; timeout may need adjusting.
sortAsc	Default TRUE returns CID lists sorted in ascending order (lowest CID first), FALSE reverts to the eUtils default of highest CID first.
timeout	The timeout, in seconds.

Value

Either a count of CIDs or a vector of CIDs (NA if error).

Author(s)

Emma Schymanski <[e-mail]>

References

PubChem search: http://pubchem.ncbi.nlm.nih.gov/

Entrez eUtils: https://www.ncbi.nlm.nih.gov/books/NBK25500/ and https://www.ncbi.nlm.nih.gov/books/NBK25499/

Examples

getPcCand.ExactMass(298.095947)
getPcCand.ExactMass(298.095947,5,CountOnly=F)
getPcCand.ExactMass(298.095947,5,CountOnly=F,sortAsc=F)
getPcCand.ExactMass(298.095947,5,CountOnly=F,sortAsc=T,RetMax=10)
# invalid mass entries will return an error in the mass calc
getPcCand.ExactMass("298.095947")

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.