rename.SRA.files: Rename SRA files from metadata
In ORFik: Open Reading Frames in Genomics
Description
Usage
Arguments
Value
See Also
Description
Rename SRA files from metadata
Usage
1
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:
download.SRA.metadata(),
download.SRA(),
download.ebi(),
install.sratoolkit()
ORFik documentation built on March 27, 2021, 6 p.m.
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Description Usage Arguments Value See Also
Description
Rename SRA files from metadata
Usage
1 | 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:
download.SRA.metadata(),
download.SRA(),
download.ebi(),
install.sratoolkit()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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