qualityMask: Mask bases by quality
In MarioniLab/sarlacc: Pipeline for Oxford Nanopore RNA-Seq Data Analysis
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
Mask out low-quality bases in a DNA sequence prior to downstream analyses.
Usage
1
qualityMask(seq, max.err)
Arguments
seq
A QualityScaledDNAStringSet containing one or more sequences with quality strings.
max.err
Numeric scalar specifying the error probability threshold, above which bases are to be masked.
Value
A DNAStringSet containing masked DNA sequences.
All bases with error probabilities above max.err will be replaced with Ns.
Author(s)
Aaron Lun
See Also
Examples
1
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X <- QualityScaledDNAStringSet(
DNAStringSet(paste0("ACAGCTGCTGCAGCTGTG")),
PhredQuality(rbeta(18, 1, 10))
)
qualityMask(X, max.err=0.5)
qualityMask(X, max.err=0.1)
qualityMask(X, max.err=0.01)
MarioniLab/sarlacc documentation built on May 13, 2019, 12:51 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
Mask out low-quality bases in a DNA sequence prior to downstream analyses.
Usage
1 | qualityMask(seq, max.err)
|
Arguments
seq |
A QualityScaledDNAStringSet containing one or more sequences with quality strings. |
max.err |
Numeric scalar specifying the error probability threshold, above which bases are to be masked. |
Value
A DNAStringSet containing masked DNA sequences.
All bases with error probabilities above max.err will be replaced with Ns.
Author(s)
Aaron Lun
See Also
Examples
1 2 3 4 5 6 7 8 | X <- QualityScaledDNAStringSet(
DNAStringSet(paste0("ACAGCTGCTGCAGCTGTG")),
PhredQuality(rbeta(18, 1, 10))
)
qualityMask(X, max.err=0.5)
qualityMask(X, max.err=0.1)
qualityMask(X, max.err=0.01)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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