SFFRead-class {R453Plus1Toolbox} | R Documentation

## Class `"SFFRead"`

### Description

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

### Objects from the Class

Objects can be created by calls of the form `new("SFFRead", ...)`. Usually, objects will be created by calling the `getRead` method on an object of class `SFFContainer`.

### Slots

`name`:

  Object of class `"character"` representing the name of the read.

`read`:

  Object of class `"DNAString"` containing the basecalled nucleotide sequence of the read.

`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. 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. 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. 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. 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.

`flowgram`:

  Object of class `"numeric"` containing the homopolymer stretch estimates for each flow.

`flowIndexes`:

  Object of class `"numeric"` 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.

`quality`:

  Object of class `"BString"` containing the quality scores for each of the bases in the sequence, where the values use the standard -log10 probability scale.

### Methods

read<-

  `signature(object = "SFFRead", value = "DNAString")`: Setter-method for the read slot.

read

  `signature(object = "SFFRead")`: Getter-method for the read 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.

keySequence<-

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

keySequence

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

clipAdapterLeft<-

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

clipAdapterLeft

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

clipAdapterRight<-

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

clipAdapterRight

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

clipQualityLeft<-

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

clipQualityLeft

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

clipQualityRight<-

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

clipQualityRight

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

flowgram<-

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

flowgram

  `signature(object = "SFFRead")`: Getter-method for the flowgram slot.

flowIndexes<-

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

flowIndexes

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

name<-

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

name

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

quality<-

  `signature(object = "SFFRead", value = "BString")`: Setter-method for the quality slot.

quality

  `signature(object = "SFFRead")`: Getter-method for the quality slot.

### Author(s)

Christian Ruckert

### See Also

`readSFF`, `SFFContainer`

### Examples

    showClass("SFFRead")

[Package R453Plus1Toolbox version 1.40.0 Index]