read.abif: Read ABIF formatted files

In MLPA: Multiplex Ligation-Dependent Probe Amplification Data Analysis

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)

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.

Details

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

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.

Note

This function and the current help page were duplicated from the seqinr package in its 3.0-7 version (available on the CRAN under GPL 2 licensing).

Author(s)

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

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 http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf. Last visited on 2018-03-27.

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/A5918.fsa", package="MLPA"))

MLPA documentation built on May 2, 2020, 1:06 a.m.