findFa {ORFik}

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.wiggle(), fimport(), fread.bed(), optimizeReads(), readBam(), readBigWig(), readWig()

Examples

# Some fasta genome with existing fasta index in same folder
path <- system.file("extdata/Danio_rerio_sample", "genome_dummy.fasta", package = "ORFik")
findFa(path)

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