download.SRA.metadata: Downloads metadata from SRA

Description Usage Arguments Value References See Also Examples

View source: R/SRA_helper.R

Description

Downloads metadata from SRA

Usage

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download.SRA.metadata(SRP, outdir, remove.invalid = TRUE)

Arguments

SRP

a string, a study ID as either the SRP, ERP, DRP or PRJ of the study, examples would be "SRP226389" or "ERP116106".

outdir

directory to save file, The file will be called "SraRunInfo_SRP.csv", where SRP is the SRP argument. The directory will be created if not existing.

remove.invalid

logical, default TRUE. Remove Runs with 0 reads (spots)

Value

a data.table of the opened file

References

doi: 10.1093/nar/gkq1019

See Also

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

Examples

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## Originally on SRA
outdir <- tempdir() # Specify output directory
# download.SRA.metadata("SRP226389", outdir)
## ORiginally on ENA
# download.SRA.metadata("ERP116106", outdir)

ORFik documentation built on March 27, 2021, 6 p.m.