findFa: Convenience wrapper for Rsamtools FaFile
In JokingHero/ORFik: Open Reading Frames in Genomics
View source: R/utils_imports.R
findFa R Documentation
Convenience wrapper for Rsamtools FaFile
Description
Get fasta file object, to find sequences in file.
Will load and import file if necessarry.
Usage
findFa(faFile)
Arguments
faFile
FaFile, BSgenome, fasta/index file path or an
ORFik experiment. This file is usually used to find the
transcript sequences from some GRangesList.
Value
a FaFile or BSgenome
See Also
Other utils:
bedToGR(),
convertToOneBasedRanges(),
export.bed12(),
export.bigWig(),
export.fstwig(),
export.wiggle(),
fimport(),
fread.bed(),
optimizeReads(),
readBam(),
readBigWig(),
readWig()
Examples
# Some fasta genome with existing fasta index in same folder
path <- system.file("extdata/references/danio_rerio", "genome_dummy.fasta", package = "ORFik")
findFa(path)
JokingHero/ORFik documentation built on April 23, 2024, 12:37 a.m.
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View source: R/utils_imports.R
| findFa | R Documentation |
Convenience wrapper for Rsamtools FaFile
Description
Get fasta file object, to find sequences in file.
Will load and import file if necessarry.
Usage
findFa(faFile)
Arguments
faFile |
|
Value
a FaFile or BSgenome
See Also
Other utils:
bedToGR(),
convertToOneBasedRanges(),
export.bed12(),
export.bigWig(),
export.fstwig(),
export.wiggle(),
fimport(),
fread.bed(),
optimizeReads(),
readBam(),
readBigWig(),
readWig()
Examples
# Some fasta genome with existing fasta index in same folder
path <- system.file("extdata/references/danio_rerio", "genome_dummy.fasta", package = "ORFik")
findFa(path)
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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