FSAtools (version 2.0.5)

read.abif: Read ABIF formatted files

Description

ABIF stands for Applied Biosystem Inc. Format, a binary format modeled after TIFF format. Corresponding files usually have an *.ab1 or *.fsa extension.

Usage

read.abif(filename, max.bytes.in.file = file.info(filename)$size,
    pied.de.pilote = 1.2, verbose = FALSE)

Value

A list with three components: Header which is a list that contains various low-level information, among which numelements is the number of elements in the directory and dataoffset the offset to find the location of the directory. Directory is a data.frame for the directory of the file with the number of row being the number of elements in the directory and the 7 columns describing various low-level information about the elements. Data is a list with the number of components equal to the number of elements in the directory.

Arguments

filename

The name of the file.

max.bytes.in.file

The size in bytes of the file, defaulting to what is returned by file.info

pied.de.pilote

Safety factor: the argument n to readBin is set as pied.de.pilote*max.bytes.in.file.

verbose

logical [FALSE]. If TRUE verbose mode is on.

Author

J.R. Lobry, 'bool' type implemented by Sylvain Mareschal

Details

All data are imported into memory, there is no attempt to read items on the fly.

References

Charif, D. and Lobry, J.R. (2007) Structural approaches to sequence evolution: Molecules, networks, populations ISBN 978-3-540-35305-8, pp 207-232.

Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format. Available at https://projects.nfstc.org/workshops/resources/articles/ABIF_File_Format.pdf. Last visited on 2020-07-10.

See Also

readBin which is used here to import the binary file and file.info to get the size of the file.

Examples

  # Example FSA file provided
  rawFsa <- read.abif(system.file("extdata/fsa_GEP/A5918.fsa", package="FSAtools"))