getQueryCounts: Return query counts for batch PubMed queries
In seandavi/Rpressa: A collection of useful code for bioinformatics

Description Usage Arguments Value Author(s) References See Also Examples

Trying to discover the biological meaning of a set of genes can be challenging. This function simply does batch PubMed queries and returns a matrix of record counts in matrix form with genes as rows and terms as columns.

1	getQueryCounts(genes, terms, baseline=NULL)

`genes`	A character vector of gene names (or miRNAs, etc.). These will become the rows of the query count matrix returned.
`terms`	A character vector of terms to pair with each gene. These will become the columns of the query count matrix returned.
`baseline`	A string to include with ALL queries.

A list with three items:

A vector of the number of of pubmed results for each gene, including the baseline terms if specified

A vector of the number of of pubmed results for each term, including the baseline terms if specified

A numeric matrix with column names taken from "terms" and row names taken from "genes". Each entry in the matrix is the count of records in PubMed for that pair of gene/term.

Sean Davis <sdavis2@mail.nih.gov>

http://www.ncbi.nlm.nih.gov/pubmed/

pubmedQuery

genes = c('BRCA1','AKT','PIK3CA','CDKN2A')
terms = c('cancer','cell cycle','tumor suppressor','oncogene')
qcounts = getQueryCounts(genes,terms)
qcounts