read.fsa: Get fluorescence data from fsa files

Description Usage Arguments Value Author(s) See Also

View source: R/readfsa.R

Description

Read fluorescence data from fsa files.

Usage

1
2
3
  read.fsa(path = "./", files = NULL, dye, SizeStandard,
    Breaks = NULL, Range = range(SizeStandard),
    binwidth = 1, SNR = 20, verbose = TRUE)

Arguments

files

A vector of filenames. Can be a relative or an absolute path.

path

The base path for the filenames. Defaults to the working directory.

dye

A vector with the names of the dyes used for the data.

SizeStandard

A numeric vector with basepairs of the size standard.

Breaks

A named list with the breaks used for binning the fluorescence. If missing the breaks are estimated by read.fsa.bins()

Range

A numeric vector of length 2 with the lower and upper limit of the desired markers (in number of base pairs).

binwidth

The desired width of the bins.

SNR

Maximum signal-to-noise ratio for peaks of the size standard. Used to ignore unwanted very strong peaks.

verbose

Print the name of each file when processing it. Useful for tracking progress.

Value

A data.frame with 5 variables: Filename, Dye, Marker, Binwidth and Fluorescence.

Author(s)

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

See Also

read.fsa.bins


AFLP documentation built on May 2, 2019, 6:13 p.m.