File formats are a unified way which softwares would know how to open and evaluate the content.

Tabular formats

Export data into easy to read formats

  • Ideally - Save data in plain text files.
    eg in Excel (one sheet per file): File -> Save As -> File Format:

Comma-separated Values (.csv)

chr,position,orientation
chr1,89009884,+
chrX,14400933,-


Tab-delimited Text (.txt)

date    patientID   proviral_load
2023-07-01    M100544   100
2023-10-01    F123455   40


  • R has packages for reading excel files (recommended only if has to be multi-sheet).


Non-tabular formats

General formats

Will not be covered here, but you may come across them - e.g. XML, JSON, TOML - often have dedicated packages for reading into R.

Biological formats

Will not be covered here, but you may come across them - e.g. VCF, SAM, FASTA - often have dedicated packages for reading into R - search https://www.bioconductor.org