genotypeFasta

<code>genotypeFasta</code> converts a genotype table into a vector of nucleotide
sequences.

Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of
any novel alleles. This information is then used to correct existing V
allele calls from among the sample sequences.
Citations:
Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>,
Gadala-Maria, et al (2019) <doi:10.3389/fimmu.2019.00129>.

Susanna Marquez

tigger

Infers Novel Immunoglobulin Alleles from Sequencing Data

Daniel Gadala-Maria

Moriah Cohen

Jason Vander Heiden

Gur Yaari

Steven Kleinstein

genotypeFasta function

<dl><dt>genotype</dt>
<dd><code>data.frame</code> of alleles denoting a genotype, 
as returned by inferGenotype.</dd>
<dt>germline_db</dt>
<dd>vector of named nucleotide germline sequences
matching the alleles detailed in <code>genotype</code>.</dd>
<dt>novel</dt>
<dd>an optional <code>data.frame</code> containing putative
novel alleeles of the type returned by
findNovelAlleles.</dd></dl>

Arguments

Return the nucleotide sequences of a genotype — genotypeFasta

<dl>

<dt>genotype</dt>
<dd><code>data.frame</code> of alleles denoting a genotype, 
as returned by inferGenotype.</dd>


<dt>germline_db</dt>
<dd>vector of named nucleotide germline sequences
matching the alleles detailed in <code>genotype</code>.</dd>


<dt>novel</dt>
<dd>an optional <code>data.frame</code> containing putative
novel alleeles of the type returned by
findNovelAlleles.</dd>

</dl>

genotypeFasta: Return the nucleotide sequences of a genotype

Description

Usage

Value

Arguments

See Also

Examples