GappedReads-class: (Legacy) GappedReads objects
In GenomicAlignments: Representation and manipulation of short genomic alignments
Description
Constructor
Accessors
Author(s)
References
See Also
Examples
Description
The GappedReads class extends the GAlignments class.
A GappedReads object contains all the information contained in a
GAlignments object plus the sequences of the queries.
Those sequences can be accessed via the qseq accessor.
Constructor
GappedReads objects are typically created when reading a file
containing aligned reads with the readGappedReads
function.
Accessors
In the code snippets below, x is a GappedReads object.
-
qseq(x):
Extracts the sequences of the queries as a
DNAStringSet object.
Author(s)
Hervé Pagès
References
http://samtools.sourceforge.net/
See Also
-
GAlignments objects.
-
readGappedReads.
Examples
1
2
3
4
greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
greads <- readGappedReads(greads_file)
greads
qseq(greads)
GenomicAlignments documentation built on Nov. 8, 2020, 8:12 p.m.
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Description Constructor Accessors Author(s) References See Also Examples
Description
The GappedReads class extends the GAlignments class.
A GappedReads object contains all the information contained in a
GAlignments object plus the sequences of the queries.
Those sequences can be accessed via the qseq accessor.
Constructor
GappedReads objects are typically created when reading a file
containing aligned reads with the readGappedReads
function.
Accessors
In the code snippets below, x is a GappedReads object.
-
qseq(x): Extracts the sequences of the queries as aDNAStringSetobject.
Author(s)
Hervé Pagès
References
http://samtools.sourceforge.net/
See Also
-
GAlignments objects.
-
readGappedReads.
Examples
1 2 3 4 | greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
greads <- readGappedReads(greads_file)
greads
qseq(greads)
|
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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