readSAGA: Append fluorescence data from a SAGA file to an AFLP object

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Append fluorescence data from a SAGA file to an AFLP object.

Usage

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  readSAGA(filename, add.to, maxMissing = 0.25,
    textclean = function(x) {     x })

Arguments

filename

The SAGA file to be imported.

add.to

The AFLP object were the fluorescence is appended to.

maxMissing

A relative threshold. If more than this ratio of replicates have missing data, then no data is appended.

textclean

A user defined function to alter the names of the replicates after reading the SAGA file. Only useful when the names in the SAGA files do not match with the names in the AFLP object. Directly using the correct names is SAGA solves a lot of problems.

Details

NOTE: the SAGA file must be in the default CSV format.

Value

Return an AFLP object. If add.to is an AFLP object, then the fluorescence data is appended to it. Otherwise a new AFLP object is created.

Author(s)

Thierry Onkelinx Thierry.Onkelinx@inbo.be, Paul Quataert

See Also

as.AFLP

Examples

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data(TiliaDesign)
 Tilia <- as.AFLP(TiliaDesign)
 Tilia <- readSAGA(
   system.file("extdata", "Tilia_bandvaluespc1", package = "AFLP"),
   add.to = Tilia
 )
 Tilia <- readSAGA(
   system.file("extdata", "Tilia_bandvaluespc2", package = "AFLP"),
   add.to = Tilia
 )
 Tilia <- readSAGA(
   system.file("extdata", "Tilia_bandvaluespc3", package = "AFLP"),
   add.to = Tilia
 )
 Tilia <- readSAGA(
   system.file("extdata", "Tilia_bandvaluespc4", package = "AFLP"),
   add.to = Tilia
 )


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