read.fsa: Imports a .fsa file from Applied Biosystems

In FSAtools: Fragment Analysis and Capillary Sequencing Tool Kit

Imports a .fsa file from Applied Biosystems

Description

This function parses a FSA file holding fragment analysis data, using seqinr package's read.abif.

Usage

  read.fsa(file, lowess = TRUE, lowess.top = 200, processed = FALSE, meta.extra = NULL,
    quiet = FALSE, ...)

Arguments

file	Single character value, the name and path of the file to parse.
lowess	Single logical value, whether to apply lowess on intensities to smooth time-related biases or not.
lowess.top	Single numeric value, values flagged as "off-scale" or above this threshold will be replaced by lowess.top to compute the lowess smooth, in order to limit the impact of high and wide peaks.
processed	Single logical value, whether to use processed DATA values (as stored in sets 9 to 12, not always available) rather than raw values (sets 1 to 4). If NA, processed ones will be used as long as they are available, else raw ones will be used instead.
meta.extra	Named character vector, defining which extra fields to extract to populate the runMetaData attribute. The vector names define the human-readable names to use in output, the vector values provide the 4 uppercase letter code to extract (all values will be gathered in a vector if the code is used several times). See the reference provided in read.abif for existing codes in the ABIF file format.
quiet	Single logical value, whether to print FSA meta-data read from the file or not.
...	Further arguments to be passed to read.abif.

Value

A S3 object of class fsa

Author(s)

Sylvain Mareschal

See Also

read.abif, generic.process, plot.fsa, read.sanger

Examples

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

FSAtools documentation built on Aug. 19, 2023, 1:06 a.m.