QualityReport-class: QualityReport

In roblanf/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

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)

roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.