QualityScore: Construct objects indicating read or alignment quality
In ShortRead: FASTQ input and manipulation
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
Use these functions to construct quality indicators for reads or
alignments. See QualityScore for details of
object content and methods available for manipulating them.
Usage
1
2
3
4
5
NumericQuality(quality = numeric(0))
IntegerQuality(quality = integer(0))
MatrixQuality(quality = new("matrix"))
FastqQuality(quality, ...)
SFastqQuality(quality, ...)
Arguments
quality
An object used to initialize the data
structure. Appropriate objects are indicated in the constructors
above for Numeric, Integer, and Matrix qualities. For
FastqQuality and SFastqQuality, methods are defined
for BStringSet,
character, and missing.
...
Additional arguments, currently unused.
Value
Constructors return objects of the corresponding class derived from
QualityScore.
Author(s)
Martin Morgan <mtmorgan@fhcrc.org>
See Also
QualityScore, readFastq,
readAligned
Examples
1
2
3
4
nq <- NumericQuality(rnorm(20))
nq
quality(nq)
quality(nq[10:1])
ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
Use these functions to construct quality indicators for reads or
alignments. See QualityScore for details of
object content and methods available for manipulating them.
Usage
1 2 3 4 5 | NumericQuality(quality = numeric(0))
IntegerQuality(quality = integer(0))
MatrixQuality(quality = new("matrix"))
FastqQuality(quality, ...)
SFastqQuality(quality, ...)
|
Arguments
quality |
An object used to initialize the data
structure. Appropriate objects are indicated in the constructors
above for Numeric, Integer, and Matrix qualities. For
|
... |
Additional arguments, currently unused. |
Value
Constructors return objects of the corresponding class derived from
QualityScore.
Author(s)
Martin Morgan <mtmorgan@fhcrc.org>
See Also
QualityScore, readFastq,
readAligned
Examples
1 2 3 4 | nq <- NumericQuality(rnorm(20))
nq
quality(nq)
quality(nq[10:1])
|
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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