createHaplotypeTable

<code>createHaplotypeTable</code> Haplotype of a specific gene

Infers V-D-J (Variable-Diversity-Joining) haplotypes and gene
deletions from AIRR-seq (Adaptive Immune Receptor Repertoire sequencing)
data for Ig (Immunoglobulin) and TR (T cell Receptor) chains, based on J
(Joining), D (Diversity), or V (Variable) genes as anchor, by adapting a
Bayesian framework.
It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene.
Citation:
Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>.
Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.

Ayelet Peres

rabhit

Inference Tool for Antibody Haplotype

Moriah Gidoni

Gur Yaari

createHaplotypeTable function

<dl><dt>df</dt>
<dd>table of counts</dd>
<dt>HapByPriors</dt>
<dd>vector of frequencies of each of the anchor gene alleles</dd>
<dt>toHapByCol</dt>
<dd>logical, haplotype each chromosome separetly to imrove the aligner assignmnet</dd>
<dt>toHapPriors</dt>
<dd>vector of frequencies of the haplotyped gene alleles</dd></dl>

Arguments

Create haplotype table — createHaplotypeTable

<dl>

<dt>df</dt>
<dd>table of counts</dd>


<dt>HapByPriors</dt>
<dd>vector of frequencies of each of the anchor gene alleles</dd>


<dt>toHapByCol</dt>
<dd>logical, haplotype each chromosome separetly to imrove the aligner assignmnet</dd>


<dt>toHapPriors</dt>
<dd>vector of frequencies of the haplotyped gene alleles</dd>

</dl>

createHaplotypeTable: Create haplotype table

Description

Usage

Value

Arguments