citationCheck: Check pubmed citations for genes

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Check pubmed citations for genes

Description

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.

Usage

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

Author(s)

Nicholas Mikolajewicz

See Also

EUtilsSummary

Examples

m8.citations <- citationCheck(gene.query = gene.list$m8, search.query = "hematopoietic|hematogenic|HSC", delay = 0.5,
mindate=2000, maxdate=2021, verbose = T)

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.