PipetteFile-class: File extension classes

In steinbaugh/brio: Pipette Biological Data In and Out of R

File extension classes

Description

Currently intended for use with import function.

Primary classes

• PipetteBamFile: Binary sequence alignment map (BAM).

• PipetteBcfFile: Binary variant call format (BCF).

• PipetteBcbioCountsFile: bcbio-nextgen counts file.

• PipetteCramFile: Compressed reference-oriented alignment map (CRAM).

• PipetteCsvFile: Comma-separated values file (CSV).

• PipetteFastaFile: FASTA file.

• PipetteFastqFile: FASTQ file.

• PipetteGafFile: Gene Ontology (GO) annotation file (GAF).

• PipetteGctFile: Gene Cluster Text file (GCT).

• PipetteGmtFile: Gene matrix transposed file (GMT).

• PipetteGmxFile: Gene matrix file (GMX).

• PipetteGrpFile: Gene set file (GRP).

• PipetteJsonFile: JSON file.

• PipetteMafFile: Mutation annotation format file (MAF).

• PipetteMtxFile: MatrixMarket exchange file (MTX).

• PipetteOboFile: Open Biomedical Ontologies file (OBO).

• PipettePzfxFile: GraphPad Prism file (PZFX).

• PipetteRdsFile: R data file containing a single, serialized object (RDS).

• PipetteRDataFile: R Data file containing multiple objects (RData/RDA).

• PipetteSamFile: Sequence alignment map (SAM).

• PipetteTsvFile: Tab-separated values file (TSV).

• PipetteTableFile: Base R table file (TXT).

• PipetteVcfFile: Variant call format (VCF).

• PipetteYamlFile: YAML file.

PipetteDelimFile-class

Delimited file.

File extension group supporting:

• CSV: Comma-separated values

• TSV: Tab-separated values

• Base R table (TXT)

PipetteExcelFile-class

Microsoft Excel file.

File extension group supporting:

• XLS

• XLSB

• XLSX

PipetteLinesFile-class

Source code lines file.

File extension group supporting:

• BASH: Bash shell script

• LOG: Log file

• MD: Markdown file

• PY: Python script

• R: R script

• RMD: R Markdown file

• SH: Shell script (e.g. Bash, POSIX)

• ZSH: Zsh shell script

PipetteRioFile-class

File extension supported by rio::import.

File extension group supporting:

• ARFF: Weka Attribute-Relation File Format

• DBF: dBase Database File

• DIF: Data Interchange Format

• DTA: Stata

• FWF: Fixed-width formatting

• MAT: Matlab

• MTP: Minitab

• ODS: OpenDocument (LibreOffice)

• POR: SPSS

• PSV: Pipe-separated values

• SAS7BDAT: SASS

• SAV: SPSS

• SYD: Systat

• REC: Epi Info

• XPT: SASS

PipetteRtracklayerFile-class

File extension supported by rtracklayer::import.

File extension group supporting:

• BED, BED15, BEDGRAPH, BEDPE

• BIGWIG, BW, WIG

• GFF, GFF1, GFF2, GFF3, GTF

• BROADPEAK, NARROWPEAK

Note

Updated 2023-12-13.

steinbaugh/brio documentation built on Feb. 1, 2024, 6:42 p.m.