reverseComplement

reverseComplement,character-method

Whereas the <code>reverseComplement</code> function available in Biostrings only
functions on <code>XString</code> and <code>XStringSet</code> objects, the version in
polyRAD also works on character strings. It is written as an S4 method
in order to avoid conflict with Biostrings. It is primarily included for
internal use by polyRAD, but may be helpful at the user level as well.

Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis. 'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Lindsay V. Clark

polyRAD

Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids

U.S. National Science Foundation 

reverseComplement function

<dl> <dt>x</dt>
<dd>A vector of character strings indicating DNA sequence using IUPAC codes.</dd> <dt>...</dt>
<dd>Additional arguments (none implemented)</dd></dl>

Arguments

Author

Reverse Complement of DNA Sequence Stored as Character String — reverseComplement

<dl>

 <dt>x</dt>
<dd>A vector of character strings indicating DNA sequence using IUPAC codes.</dd>

 <dt>...</dt>
<dd>Additional arguments (none implemented)</dd>

</dl>

reverseComplement: Reverse Complement of DNA Sequence Stored as Character String

Description

Usage

Value

Arguments

Author

See Also

Examples