SFFContainer-class {R453Plus1Toolbox} | R Documentation

## Class `"SFFContainer"`

### Description

This class is a container for data from files in Roche's Standard Flowgram Format (SFF).

### Objects from the Class

Objects can be created by calls of the form `new("SFFContainer", ...)`. Usually, objects will be created by calling the `readSFF` method on a file in SFF format.

### Slots

`name`:

  Object of class `"character"` containing the name of the file this SFFContainer was created from.

`flowgramFormat`:

  Object of class `"numeric"` representing the format used to encode each of the flowgram values for each read. Currently, only one flowgram format has been adopted and is coded by the value 1.

`flowChars`:

  Object of class `"character"` containing the array of nucleotide bases ('A', 'C', 'G', 'T') that correspond to the nucleotides used for each flow of each read.

`keySequence`:

  Object of class `"character"` representing the nucleotide bases of the key sequence used for these reads.

`clipQualityLeft`:

  Object of class `"numeric"` representing the position of the first base after the clipping point for an attached quality sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityLeft. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

`clipQualityRight`:

  Object of class `"numeric"` representing the position of the last base before the clipping point for an attached quality sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityRight. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

`clipAdapterLeft`:

  Object of class `"numeric"` representing the position of the first base after the clipping point for an attached adapter sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityLeft. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

`clipAdapterRight`:

  Object of class `"numeric"` representing the position of the last base before the clipping point for an attached adapter sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityRight. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

`flowgrams`:

  Object of class `"list"` containing the homopolymer stretch estimates for each flow using one list item for each read.

`flowIndexes`:

  Object of class `"list"` containing the flow positions for each base in the called sequence, i.e. for each base, the position in the flowgram whose estimate resulted in that base being called. Each read has its own list item.

`reads`:

  Object of class `"QualityScaledDNAStringSet"` containing the basecalled nucleotide sequences of each read together with the quality scores for each of the bases in the sequence using the standard -log10 probability scale.

### Methods

addRead

  `signature(object = "SFFContainer", read = "SFFRead")`: Adds an object of class `SFFRead` to the `SFFContainer`

getRead

  `signature(object = "SFFContainer", readname = "character")`: Returns the read with the given name as an object of class `SFFRead`.

clipAdapterLeft<-

  `signature(object = "SFFContainer", value = "numeric")`: Setter-method for the clipAdapterLeft slot.

clipAdapterLeft

  `signature(object = "SFFContainer")`: Getter-method for the clipAdapterLeft slot.

clipAdapterRight<-

  `signature(object = "SFFContainer", value = "numeric")`: Setter-method for the clipAdapterRight slot.

clipAdapterRight

  `signature(object = "SFFContainer")`: Getter-method for the clipAdapterRight slot.

clipQualityLeft<-

  `signature(object = "SFFContainer", value = "numeric")`: Setter-method for the clipQualityLeft slot.

clipQualityLeft

  `signature(object = "SFFContainer")`: Getter-method for the clipQualityLeft slot.

clipQualityRight<-

  `signature(object = "SFFContainer", value = "numeric")`: Setter-method for the clipQualityRight slot.

clipQualityRight

  `signature(object = "SFFContainer")`: Getter-method for the clipQualityRight slot.

name<-

  `signature(object = "SFFContainer", value = "character")`: Setter-method for the name slot.

name

  `signature(object = "SFFContainer")`: Getter-method for the name slot.

flowChars<-

  `signature(object = "SFFContainer", value = "character")`: Setter-method for the flowChars slot.

flowChars

  `signature(object = "SFFContainer")`: Getter-method for the flowChars slot.

flowgramFormat<-

  `signature(object = "SFFContainer", value = "numeric")`: Setter-method for the flowgramFormat slot.

flowgramFormat

  `signature(object = "SFFContainer")`: Getter-method for the flowgramFormat slot.

flowgrams<-

  `signature(object = "SFFContainer", value = "list")`: Setter-method for the flowgrams slot.

flowgrams

  `signature(object = "SFFContainer")`: Getter-method for the flowgrams slot.

flowIndexes<-

  `signature(object = "SFFContainer", value = "list")`: Setter-method for the flowIndexes slot.

flowIndexes

  `signature(object = "SFFContainer")`: Getter-method for the flowIndexes slot.

keySequence<-

  `signature(object = "SFFContainer", value = "character")`: Setter-method for the keySequence slot.

keySequence

  `signature(object = "SFFContainer")`: Getter-method for the keySequence slot.

reads<-

  `signature(object = "SFFContainer", value = "QualityScaledDNAStringSet")`: Setter-method for the reads slot.

reads

  `signature(object = "SFFContainer")`: Getter-method for the reads slot.

[

  `signature(x = "SFFContainer", i = "ANY", j = "ANY")`: Subsetting a SFFContainer object.

### Author(s)

Christian Ruckert

### See Also

`readSFF`, `SFFRead`

### Examples

      showClass("SFFContainer")

[Package R453Plus1Toolbox version 1.38.0 Index]