Wrappers to Save Common File Formats

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Documentation for package ‘alabaster.files’ version 1.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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B C F G I L P R S T V W misc

-- B --

BamFileReference	Reference to a BAM file
BamFileReference-class	Reference to a BAM file
BamIndexWrapper	Reference to a BAM file
BamIndexWrapper-class	Reference to a BAM file
BamWrapper	Reference to a BAM file
BamWrapper-class	Reference to a BAM file
BcfFileReference	Reference to a BCF file
BcfFileReference-class	Reference to a BCF file
BedFileReference	Reference to a BED file
BedFileReference-class	Reference to a BED file
BedWrapper	Reference to a BED file
BedWrapper-class	Reference to a BED file
BgzipIndexWrapper	Wrapper for a Bgzip index file
BgzipIndexWrapper-class	Wrapper for a Bgzip index file
BigBedFileReference	Reference to a bigBed file
BigBedFileReference-class	Reference to a bigBed file
BigBedWrapper	Reference to a bigBed file
BigBedWrapper-class	Reference to a bigBed file
BigWigFileReference	Reference to a bigWig file
BigWigFileReference-class	Reference to a bigWig file
BigWigWrapper	Reference to a bigWig file
BigWigWrapper-class	Reference to a bigWig file

-- C --

CompressedIndexedWrapper-class	Virtual wrapper classes
CompressedWrapper-class	Virtual wrapper classes
compression	Virtual wrapper classes

-- F --

FaIndexWrapper	Reference to a FASTA file
FaIndexWrapper-class	Reference to a FASTA file
FastaFileReference	Reference to a FASTA file
FastaFileReference-class	Reference to a FASTA file
FastaWrapper	Reference to a FASTA file
FastaWrapper-class	Reference to a FASTA file
FastqFileReference	Reference to a FASTQ file
FastqFileReference-class	Reference to a FASTQ file
FastqWrapper	Reference to a FASTQ file
FastqWrapper-class	Reference to a FASTQ file
FileReference	Virtual file reference class
FileReference-class	Virtual file reference class

-- G --

GffFileReference	Reference to a GFF file
GffFileReference-class	Reference to a GFF file
GffWrapper	Reference to a GFF file
GffWrapper-class	Reference to a GFF file
GmtFileReference	Reference to a GMT file
GmtFileReference-class	Reference to a GMT file
GmtWrapper	Reference to a GMT file
GmtWrapper-class	Reference to a GMT file

-- I --

index	Virtual wrapper classes
index-method	Virtual wrapper classes
IndexedWrapper-class	Virtual wrapper classes

-- L --

loadBamIndexWrapper	Reference to a BAM file
loadBamWrapper	Reference to a BAM file
loadBedWrapper	Reference to a BED file
loadBgzipIndexWrapper	Wrapper for a Bgzip index file
loadBigBedWrapper	Reference to a bigBed file
loadBigWigWrapper	Reference to a bigWig file
loadFaIndexWrapper	Reference to a FASTA file
loadFastaWrapper	Reference to a FASTA file
loadFastqWrapper	Reference to a FASTQ file
loadGffWrapper	Reference to a GFF file
loadGmtWrapper	Reference to a GMT file
loadTabixIndexWrapper	Wrapper for a Tabix file
loadVcfWrapper	Reference to a BCF file

-- P --

path	Virtual wrapper classes
path-method	Virtual file reference class
path-method	Virtual wrapper classes

-- R --

readBamFileReference	Reference to a BAM file
readBcfFileReference	Reference to a BCF file
readBedFileReference	Reference to a BED file
readBigBedFileReference	Reference to a bigBed file
readBigWigFileReference	Reference to a bigWig file
readFastaFileReference	Reference to a FASTA file
readFastqFileReference	Reference to a FASTQ file
readGffFileReference	Reference to a GFF file
readGmtFileReference	Reference to a GMT file

-- S --

saveObject-method	Reference to a BAM file
saveObject-method	Reference to a BCF file
saveObject-method	Reference to a BED file
saveObject-method	Reference to a bigBed file
saveObject-method	Reference to a bigWig file
saveObject-method	Reference to a FASTA file
saveObject-method	Reference to a FASTQ file
saveObject-method	Reference to a GFF file
saveObject-method	Reference to a GMT file
show-method	Reference to a FASTA file
show-method	Reference to a FASTQ file
show-method	Virtual file reference class
show-method	Virtual wrapper classes
stageObject-method	Reference to a BAM file
stageObject-method	Reference to a BCF file
stageObject-method	Reference to a BED file
stageObject-method	Wrapper for a Bgzip index file
stageObject-method	Reference to a bigBed file
stageObject-method	Reference to a bigWig file
stageObject-method	Reference to a FASTA file
stageObject-method	Reference to a FASTQ file
stageObject-method	Reference to a GFF file
stageObject-method	Reference to a GMT file
stageObject-method	Wrapper for a Tabix file

-- T --

TabixIndexWrapper	Wrapper for a Tabix file
TabixIndexWrapper-class	Wrapper for a Tabix file

-- V --

VcfWrapper	Reference to a BCF file
VcfWrapper-class	Reference to a BCF file
virtual-wrapper	Virtual wrapper classes

-- W --

Wrapper-class

Virtual wrapper classes

-- misc --

$-method	Virtual file reference class
$<--method	Virtual file reference class
[[-method	Virtual file reference class
[[<--method	Virtual file reference class