updateQualityParam {sangeranalyseR}

R Documentation

Method updateQualityParam

Description

Method updateQualityParam

Usage

updateQualityParam(
  object,
  TrimmingMethod = "M1",
  M1TrimmingCutoff = 1e-04,
  M2CutoffQualityScore = NULL,
  M2SlidingWindowSize = NULL,
  ...
)

Arguments

object	A QualityReport, SangerRead, SangerContig, or 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.
...	Further updateQualityParam-related parameters.

Value

A QualityReport, SangerRead, SangerContig, or SangerAlignment instance.

Examples

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

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