rename.SRA.files: Rename SRA files from metadata

In JokingHero/ORFik: Open Reading Frames in Genomics

Rename SRA files from metadata

Description

Rename SRA files from metadata

Usage

rename.SRA.files(files, new_names)

Arguments

files

a character vector, with full path to all the files

new_names

a character vector of new names or a data.table with metadata to use to rename (usually from SRA metadata). Priority of renaming from the metadata is to check for unique names in the LibraryName column, then the sample_title column if no valid names in LibraryName. If found and still duplicates, will add "_rep1", "_rep2" to make them unique. Paired end data will get a extension of _p1 and _p2. If no valid names, will not rename, that is keep the SRR numbers, you then can manually rename files to something more meaningful.

Value

a character vector of new file names

See Also

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

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