extractGenes: Extract Genes

Description Usage Arguments Value Examples

View source: R/extractGenes.R

Description

Extracts the gene ids from the information scraped from the PubTator website.

Usage

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extractGenes(IDs, nCores = 2, nTries = 5)

Arguments

IDs

A list of article ids from the NCBI website.

nCores

An integer for the number of cores to use to mine the NCBI articles.

nTries

An integer for the number of times to attempt to connect to the NCBI website.

Value

A list. Each element in the list is also a list. It contains the entrez gene ids for all the genes found in each abstract.

Examples

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pmids <- scrapeIDs(dataBase = 'pubmed',
                   term = '(vivax malaria[MeSH Terms]) AND (folic acid antagonists[MeSH Terms])')

geneNames <- extractGenes(IDs = pmids,
                          nCores = 2,
                          nTries = 5)

Evatar/genescraper documentation built on Aug. 4, 2017, 6:34 a.m.