updateQualityParam {sangeranalyseR} | R Documentation |
Method updateQualityParam
updateQualityParam( object, TrimmingMethod = "M1", M1TrimmingCutoff = 1e-04, M2CutoffQualityScore = NULL, M2SlidingWindowSize = NULL, ... )
object |
A QualityReport, SangerRead, SangerContig, or SangerAlignment S4 instance. |
TrimmingMethod |
The read trimming method for this SangerRead. The value must be |
M1TrimmingCutoff |
The trimming cutoff for the Method 1. If |
M2CutoffQualityScore |
The trimming cutoff quality score for the Method 2. If |
M2SlidingWindowSize |
The trimming sliding window size for the Method 2. If |
... |
Further updateQualityParam-related parameters. |
A QualityReport
, SangerRead
, SangerContig
, or SangerAlignment
instance.
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)