Fragman (version 1.0.9)

read.abif: Read ABIF formatted files

Description

ABIF stands for Applied Biosystem Inc. Format, a binary fromat 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 readBin is set as pied.de.pilote*max.bytes.in.file.

verbose

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

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.

Details

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

References

Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Salazar W, Zalapa J. Fragman: An R package for fragment analysis. 2016. BMC Genetics 17(62):1-8.

Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format. Available at http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf. Last visited on 03-NOV-2008.

The figure in the example section is an attempt to reproduce figure 1A from:

Krawczyk, J., Goesmann, A., Nolte, R., Werber, M., Weisshaar, B. (2009) Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. Source Code for Biology and Medicine, 4:4.

Examples

# NOT RUN {
#No examples provided, please download seqinr package for going deeper in this function.

# }