SangerAlignment-class-updateQualityParam {sangeranalyseR} | R Documentation

## updateQualityParam

### Description

A SangerAlignment method which updates QualityReport parameter for each the SangerRead instance inside SangerAlignment.

### Usage

    ## S4 method for signature 'SangerAlignment'
    updateQualityParam(object,
      TrimmingMethod = "M1", M1TrimmingCutoff = 1e-04,
      M2CutoffQualityScore = NULL, M2SlidingWindowSize = NULL,
      processorsNum = NULL)

### Arguments

`object` | A SangerAlignment S4 instance.
`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`.
`processorsNum` | The number of processors to use, or NULL (the default) for all available processors.

### Value

A SangerAlignment instance.

### Examples

    data("sangerAlignmentData")
    ## Not run:
    updateQualityParam(sangerAlignmentData,
                       TrimmingMethod         = "M2",
                       M1TrimmingCutoff       = NULL,
                       M2CutoffQualityScore   = 40,
                       M2SlidingWindowSize    = 15)
    ## End(Not run)

[Package sangeranalyseR version 1.2.0 Index]