updateQualityParam-methods: Method updateQualityParam

updateQualityParamR 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)

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