download.SRA.metadata: Downloads metadata from SRA

In ORFik: Open Reading Frames in Genomics

Description

Downloads metadata from SRA

Usage

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

## 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.