seqinr (version 3.4-5)

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 n to 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. Data is a list with the number of components equal to the number of elements in the directory.

Details

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

References

citation("seqinR")

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.

See Also

readBin which is used here to import the binary file and file.info to get the size of the file. See JLO for the files used in quality check.

Examples

# NOT RUN {
#
# Quality check:
#

data(JLO)
JLO.check <- read.abif(system.file("abif/2_FAC321_0000205983_B02_004.fsa", 
  package = "seqinr"))
stopifnot(identical(JLO, JLO.check))

#
# Try to reproduce figure 1A from Krawczyk et al. 2009:
#

Krawczyk <- read.abif(system.file("abif/samplefsa2ps.fsa", 
  package = "seqinr"))$Data
x <- 1:length(Krawczyk[["DATA.1"]])
par(mar = c(2,4,2,0)+0.1, cex = 0.5)
plot(x, Krawczyk[["DATA.1"]], type = "l", col = "blue",
  ylab = "", xlab = "",
  ylim = c(-2000, 10000), cex = 0.5,
  main = "Figure 1A from Krawczyk et al. 2009",
  xaxs = "i", yaxs = "i",
  xaxt = "n", yaxt = "n")
axis(1, at = seq(2000, 24000, by = 2000))
axis(2, at = seq(-1000, 10000, by = 1000), las = 1)
lines(x, Krawczyk[["DATA.2"]], col = "green")
lines(x, Krawczyk[["DATA.3"]], col = "black")
lines(x, Krawczyk[["DATA.4"]], col = "red")

# }