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Currently intended for use with import function.

Details

Extends BiocFile defined in BiocIO package.

Note

Updated 2022-11-09.

Primary classes

  • BcbioCountsFile: bcbio-nextgen counts file.

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

  • FASTAFile: FASTA file.

  • FASTQFile: FASTQ file.

  • GCTFile: Gene Cluster Text file (GCT).

  • GMTFile: Gene matrix transposed file (GMT).

  • GMXFile: Gene matrix file (GMX).

  • GRPFile: Gene set file (GRP).

  • JSONFile: JSON file.

  • MTXFile: MatrixMarket exchange file (MTX).

  • OBOFile: Open Biomedical Ontologies file (OBO).

  • PZFXFile: GraphPad Prism file (PZFX).

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

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

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

  • TableFile: Base R table file (TXT).

  • YAMLFile: YAML file.

DelimFile-class

Delimited file.

File extension group supporting:

  • CSV: Comma-separated values

  • TSV: Tab-separated values

  • Base R table (TXT)

ExcelFile-class

Microsoft Excel file.

File extension group supporting:

  • XLS

  • XLSB

  • XLSX

LinesFile-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

RioHandoffFile-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

RtracklayerHandoffFile-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

See also