QualityReport-class {sangeranalyseR} | R Documentation

## QualityReport

### Description

An S4 class storing quality related inputs and results in a SangerRead S4 object.

### Slots

`TrimmingMethod`

  The read trimming method for this SangerRead. The value must be `"M1"` (the default) or `'M2'`.

`M1TrimmingCutoff`

  The trimming cutoff for the Method 1. If `TrimmingMethod` is `"M1"`, then the default value is `0.0001`. Otherwise, the value must be `NULL`.

`M2CutoffQualityScore`

  The trimming cutoff quality score for the Method 2. If `TrimmingMethod` is `'M2'`, then the default value is `20`. Otherwise, the value must be `NULL`. It works with `M2SlidingWindowSize`.

`M2SlidingWindowSize`

  The trimming sliding window size for the Method 2. If `TrimmingMethod` is `'M2'`, then the default value is `10`. Otherwise, the value must be `NULL`. It works with `M2CutoffQualityScore`.

`qualityPhredScores`

  The Phred quality scores of each base pairs after base calling.

`qualityBaseScores`

  The probability of incorrect base call of each base pairs. They are calculated from `qualityPhredScores`.

`rawSeqLength`

  The number of nucleotides of raw primary DNA sequence.

`trimmedSeqLength`

  The number of nucleotides of trimeed primary DNA sequence.

`trimmedStartPos`

  The base pair index of trimming start point from 5' end of the sequence.

`trimmedFinishPos`

  The base pair index of trimming finish point from 3' end of the sequence.

`rawMeanQualityScore`

  The mean quality score of the primary sequence after base calling. In other words, it is the mean of `qualityPhredScores`.

`trimmedMeanQualityScore`

  The mean quality score of the trimmed primary sequence after base calling.

`rawMinQualityScore`

  The minimum quality score of the primary sequence after base calling.

`trimmedMinQualityScore`

  The minimum quality score of the trimmed primary sequence after base calling.

`remainingRatio`

  The remaining sequence length ratio after trimming.

### Author(s)

Kuan-Hao Chao

### Examples

    inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
    A_chloroticaFFN <- file.path(inputFilesPath,
                                 "Allolobophora_chlorotica",
                                 "ACHLO",
                                 "Achl_ACHLO006-09_1_F.ab1")
    sangerReadF <- new("SangerRead",
                        inputSource           = "ABIF",
                        readFeature           = "Forward Read",
                        readFileName          = A_chloroticaFFN,
                        geneticCode           = GENETIC_CODE,
                        TrimmingMethod        = "M1",
                        M1TrimmingCutoff      = 0.0001,
                        M2CutoffQualityScore  = NULL,
                        M2SlidingWindowSize   = NULL,
                        baseNumPerRow         = 100,
                        heightPerRow          = 200,
                        signalRatioCutoff     = 0.33,
                        showTrimmed           = TRUE)
    "@"(sangerReadF, QualityReport)

[Package sangeranalyseR version 1.2.0 Index]