homopolymerFinder: Find homopolymers
In MarioniLab/sarlacc: Pipeline for Oxford Nanopore RNA-Seq Data Analysis
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Find homopolymer runs in a set of sequences.
Usage
1
Arguments
seq
A DNAStringSet object.
Details
This function will identify homopolymers in a given set of sequences, where a homopolymer is defined as a consecutive run of the same nucleotide.
It is useful for investigating the homopolymer frequency in unknown sequences such as UMIs.
If the sequence is known, it is often more informative to use homopolymerMatcher instead.
Gapped sequences are supported - gaps will be ignored when considering homopolymer runs and computing coordinates.
However, ambiguous bases are not be given special treatment, and will be handled like any other IUPAC character.
Value
An IRangesList object where each entry corresponds to a sequence in seq.
Each IRanges specifies the coordinates and length of a homopolymer run in the current sequence, along with the base being repeated.
Author(s)
Aaron Lun, with contributions from Cheuk-Ting Law
See Also
Examples
1
2
seq <- DNAStringSet(c("AAAAAGGGGGCCCCCCTTTTT", "AAAAGGGGGCCCCTTTTT"))
homopolymerFinder(seq)
MarioniLab/sarlacc documentation built on May 13, 2019, 12:51 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Find homopolymer runs in a set of sequences.
Usage
1 |
Arguments
seq |
A DNAStringSet object. |
Details
This function will identify homopolymers in a given set of sequences, where a homopolymer is defined as a consecutive run of the same nucleotide.
It is useful for investigating the homopolymer frequency in unknown sequences such as UMIs.
If the sequence is known, it is often more informative to use homopolymerMatcher instead.
Gapped sequences are supported - gaps will be ignored when considering homopolymer runs and computing coordinates. However, ambiguous bases are not be given special treatment, and will be handled like any other IUPAC character.
Value
An IRangesList object where each entry corresponds to a sequence in seq.
Each IRanges specifies the coordinates and length of a homopolymer run in the current sequence, along with the base being repeated.
Author(s)
Aaron Lun, with contributions from Cheuk-Ting Law
See Also
Examples
1 2 | seq <- DNAStringSet(c("AAAAAGGGGGCCCCCCTTTTT", "AAAAGGGGGCCCCTTTTT"))
homopolymerFinder(seq)
|
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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