get_bioproject_candidates: Query eutils for bioproject IDs

In JokingHero/ORFik: Open Reading Frames in Genomics

Query eutils for bioproject IDs

Description

The default query of Ribosome Profiling human, will result in internal entrez search of: Ribosome[All Fields] AND Profiling[All Fields] AND ("Homo sapiens"[Organism] OR human[All Fields])

Usage

get_bioproject_candidates(
  term = "Ribosome Profiling human",
  as_accession = TRUE,
  add_study_title = FALSE,
  RetMax = 10000
)

Arguments

term	character, default "Ribosome Profiling human". A space is translated into AND, that means "Ribosome AND Profiling AND human", will give same as above. To do OR operation, do: "Ribosome OR profiling OR human".
as_accession	logical, default TRUE. Get bioproject accessions: PRJNA, PRJEB, PRJDB values, or IDs (FALSE), numbers only. Accessions are usually the thing needed for most tools.
add_study_title	logical, default FALSE. If TRUE, return as data table with 2 columns: id: ID or accessions. title: The title of the study.
RetMax	integer, default 10000. How many IDs to return maximum

Value

character vector of Accessions or IDs. If add_study_title is TRUE, returns a data.table.

References

https://www.ncbi.nlm.nih.gov/books/NBK25501/

See Also

Other sra: browseSRA(), download.SRA(), download.SRA.metadata(), download.ebi(), install.sratoolkit(), rename.SRA.files()

Examples

term <- "Ribosome Profiling Saccharomyces cerevisiae"
# get_bioproject_candidates(term)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.