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

Description

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

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

A S3 object of class fsa

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.

Sylvain Mareschal

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

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