SffReads-class: Class '"SffReads"'. A class for next generation reads stored...
In msettles/rSFFreader: rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers

Description Usage Arguments Slots Extends Methods Author(s) See Also Examples

This class provides a way to store and manipulate, in a coordinated fashion, next generation reads stored in SFF files and their identifiers.

Objects from this class are created by readSff, or by calls to the constructor SffReads, as outlined below.

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## Constructor:

SffReads(sread, qualityIR, adapterIR, customIR, clipMode="raw", header)

`sread`	an object of type `"DNAStringSet"` object representing the sequence data.
`qualityIR`	an object of type `"IRanges"` object, specifying the quality clip points.
`adapterIR`	an object of type `"IRanges"` object, specifying the adapter clip points.
`customIR`	an object of type `"IRanges"` object, specifying the user custom clip points.

## qualityIR, adapterIR, and customIR are allowed to by empty

`clipMode`	a character string specifying the clipping mode to use for the object, see `availableClipModes` for more information.
`header`	a list object with sff header information, see `readSffHeader` for more information.

Slots header are inherited from SffHeader. Additional slots defined in this class are:

sread:: Object of class "DNAStringSet" containing IUPAC-standard, variable-length DNA strings representing sequence reads.
qualityIR:: Object of class "IRanges" contains the clip points associated with quality clip locations specified in the sff file read header. Clip locations are auto filled to those specified in the sff file.
adapterIR:: Object of class "IRanges" contains the clip points associated with adapter clip locations specified in the sff file read header. Clip locations are auto filled to those specified in the sff file.
customIR:: Object of class "IRanges" contains the clip points associated with custom clip locations as specified by the user. Initial object is set to empty.
clipMode:: Object of class "character" contains the current active clipMode, one of "raw", "adapter", "quality", "custom", "full". See explaination below for an expanded desription of clip modes.

Class "SffHeader", directly.

[: signature(x = "SffReads", i = "ANY", j = "missing"): This method creates a new SffReads object containing only those reads indexed by i. Additional methods on ‘[,SffReads’ do not provide additional functionality, but are present to limit appropriate use.
adapterClip: signature(object = "SffReads"): Returns an IRanges object of clip points when clipMode is set to "adapter"
adapterClip<-: signature(object = "SffReads"): Provide new adapter clip points with an IRanges object.
clipMode: signature(object = "SffReads"): returns the current active clipMode being used.
clipMode<-: signature(object = "SffReads"): set the current clip mode to one of "raw", "adapter", "quality", "full", or "custom"
customClip: signature(object = "SffReads"): Returns an IRanges object of clip points when clipMode is set to "custom"
customClip<-: signature(object = "SffReads"):Provide new custom clip points with an IRanges object.
fullClip: signature(object = "SffReads"): Returns an IRanges object of clip points when clipMode is set to "full"
length: signature(x = "SffReads"): returns a integer(1) vector describing the number of reads in this object.
width: signature(x = "SffReads"): returns an integer() vector of the widths of each read in this object.
names: signature(x = "SffReads"): access the id slot of the object returning a character vector of read names.
names<-: signature(x = "SffReads", value = "ANY"): Provide new read ids with a character() vector of same length as the object.
qualityClip: signature(object = "SffReads"): Returns an IRanges object of clip points when clipMode is set to "quality".
qualityClip<-: signature(object = "SffReads"): Provide new quality clip points with an IRanges object.
rawClip: signature(object = "SffReads"): Returns an IRanges object of clip points when clipMode is set to "full".
sread: signature(object = "ANY"): access the sread slot of object, returning a DNAStringSet object of reads.
id: signature(object = "SffReads"): this function is included to maintain compatibilty with the ShortRead class, returning a BStringSet object of read names for the object.
append: signature(x = "SffReads", values = "SffReads", length = "missing"): append the sread and id slots of values after the corresponding fields of x.
writeFasta: signature(object="SffReads", file, ...): write object to file in fasta format. See writeFasta for ... argument values.

Matt Settles with lots of code 'borrowed' from Martin Morgan's ShortRead Package

SffReadsQ and availableClipModes

showClass("SffReads")
showMethods(class="SffReads", where=getNamespace("rSFFreader"),
            inherit=FALSE)
            
sff <- readSff(system.file("extdata","Small454Test.sff",package="rSFFreader"), use.qualities=FALSE)
detail(sff)