Check pubmed citations for genes

For given topic (search query), number of publications that mention specified genes (gene.query) are tallied and returned. Based on RISmed package by Stephanie Kovalchik.

citationCheck(
  gene.query,
  search.query = NULL,
  delay = 0.5,
  mindate = 2000,
  maxdate = 2021,
  verbose = T,
  ...
)

Arguments

gene.query

Genes to query. Character vector.

search.query

Search query. Boolean expression are supported. Character vector. If search.query is not specified, the number of citations for each gene will be returned without constraining the tally to a specified topic.

delay

Delay between queries. If database is queried too fast, error is thrown. Default delay is 0.5.

mindate

Minimum of date range for search results (examples: 2002; 2002/01/01); must be supplied with maxdate.

maxdate

Maximum of date range for search results; must be supplied with mindate.

verbose

Print progress (T or F). Default is T.

...

additional arguments passed to EUtilsSummary

See also

EUtilsSummary

Author

Nicholas Mikolajewicz

Examples

m8.citations <- citationCheck(gene.query = gene.list$m8, search.query = "hematopoietic|hematogenic|HSC", delay = 0.5,
mindate=2000, maxdate=2021, verbose = T)
#> Warning: 'length(x) = 3 > 1' in coercion to 'logical(1)'
#> 2022-08-03 14:42:00: Retrieving 201959 citations that match 'hematopoietic|hematogenic|HSC' query...
#> Warning: 'length(x) = 4 > 1' in coercion to 'logical(1)'
#> Error in paste0("Retrieving citations for ", length(gene.query), " gene queries..."): object 'gene.list' not found