PipetteFile-class: File extension classes

PipetteFile-classR Documentation

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.


acidgenomics/pipette documentation built on Jan. 31, 2024, 10:32 p.m.