editFSA: View and manipulate fsa files
In plantarum/binner: Read fsa fragment files from an ABI Genetic Analzyer

Description Usage Arguments Details Value Author(s) Examples

Functions to view electropherograms, rename or remove samples, combine fsa objects and normalize data.

fsaDrop(fsa, epn)

fsaRename(fsa, epn, newname)

fsaCombine(fsa1, fsa2)

fsaNormalize(fsa)

fsa2PeakTab(fsa, dye)

## S3 method for class 'fsa'
print(fsa)

## S3 method for class 'fsa'
summary(fsa)

## S3 method for class 'fsa'
plot(fsa, epn, ...)

## S3 method for class 'electropherogram'
plot(ep, raw = FALSE, ...)

`fsa`	An fsa object, as produced by `readFSA`.
`epn`	The index of one or more samples. Can be an integer or a character string. Integers refer to samples in the order they are stored in an `fsa` object; character strings refer to them by name.
`newname`	The new name that will be applied to sample `epn`.
`fsa1`	An fsa object, as produced by `readFSA`
`fsa2`	An fsa object, as produced by `readFSA`
`dye`	Which dye to read when converting to a Peakscanner table. Valid values include "d6.FAM", "VIC, "NED" and "PET".

fsaDrop removes a sample from an fsa object.

fsaRename renames a sample in an fsa object.

fsaCombine combines two fsa objects

fsaNormalize normalizes the rfu values across each sample in the fsa.

fsa2PeakTab converts the fsa to a peakscanner-style peaks table.

fsaDrop returns an fsa object with the indicated samples removed.

fsaRename returns an fsa object with the indicated sample renamed.

fsaNormalize returns an fsa with the rfu values normalized. The values are scaled such that the sum of the rfus for each sample will equal the mean of the sum for all samples. Different dyes are normalized separately.

plot.fsa is the most convenient way to display an electropherogram. The epn argument allows you to pick which sample you wish to plot, and the raw argument determines whether you scale the lines by the raw reads (raw = TRUE), or by 'base pairs' (raw = FALSE, the default).

fsa2PeakTab converts the fsa to a peak table data.frame in a layout similar to that produced by peakscanner. The data.frame has three columns: sample.name, bp, and rfu. Each row includes the data for a single peak detected for a single sample. The rest of the chromatogram data is dropped.

Tyler Smith

## Not run: 
## The following examples assume fsa.data is an fsa object created by a
## call to readFSA()

## Remove the tenth sample
fsa.data.B <- fsaDrop(fsa.data, 10)

## Remove sample `unit3'
fsa.data.C <- fsaDrop(fsa.data, "unit3")

## Rename sample `d.x11' to `unit4'
fsa.data.D <- fsaRename(fsa.data, epn = "d.x11", newname = "unit4")

## Combine fsa objects from two different file sets
fsa.combined <- fsaCombine(fsa1 = block1, fsa2 = block2)

## Normalize the RFU data across all samples in an fsa object
fsa.norm <- fsaNormalize(fsa.data)


## End(Not run)