File Handlers for Genomic Data Analysis

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Documentation for package ‘GenomicTools.fileHandler’ version 0.1.5.9

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

Help Pages

GenomicTools.fileHandler-package	R Package To Handle Files From Genomic Data GenomicTools.fileHandler is a loose collection of I/O Functions Needed in Genomic Data Analysis
example.bed	Example Gene Annotation in Bed-Format
example.fasta	Example Sequencing Reads in fasta-Format
example.fastq	Example Sequencing Reads in fastq-Format
example.gff	Example Gene Annotation in gff-Format
example.gtf	Example Gene Annotation in gtf-Format
example.ped	Example Variant data in ped/map-Format
example.vcf	Example Variant data in vcf-Format
example2.gtf.gz	Example Gene Annotation in zipped gtf-Format
exportBed	Exporting a Bed File.
exportFA	Exporting a Fasta File.
importBed	Importing a Bed File.
importBlastTab	Import a Tab Delimited Blast Output File
importFA	Importing a Fasta File.
importFeatureCounts	Import from FeatureCounts
importFQ	Importing a Fastq File.
importGFF	importGFF
importGFF3	importGFF3
importGTF	Import a GTF File
importPED	importPED
importSTARLog	importSTARLog
importVCF	importVCF
importXML	importXML
plotTotalReads	plotTotalReads
plotUniquelyMappedReads	plotUniquelyMappedReads
prereadGTF	prereadGTF
print.bed	Print a bed Object
print.fa	Print a fa Object
print.featureCounts	Print a featureCounts Object
print.fq	Print a fq Object
print.gtf	Print a gtf Object
print.pedMap	Print a pedMap Object
print.vcf	Print a vcf Object
summary.bed	Summary of a bed Object
summary.fa	Summary of a fa Object
summary.featureCounts	Summary of a featureCounts Object
summary.fq	Summary of a fq Object
summary.gtf	Summary of a gtf Object
summary.STARLog	Summary of a STARLog Object