getGermline

getGermline get germline segment from specified receptor and segment

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

getGermline function

<dl><dt>receptor</dt>
<dd>row from AIRR-table containing sequence of interest</dd>
<dt>references</dt>
<dd>list of reference segments. Must be specific to
locus and segment</dd>
<dt>segment</dt>
<dd>Gene segment to search. Must be V, D, or J.</dd>
<dt>field</dt>
<dd>Column name for segment gene call (e.g. v_call)</dd>
<dt>germ_start</dt>
<dd>Column name of index of segment start within germline 
segment (e.g. v_germline_start)</dd>
<dt>germ_end</dt>
<dd>Similar to germ_start, but specifies end of segment 
(e.g. v_germline_end)</dd>
<dt>germ_length</dt>
<dd>Similar to germ_start, but specifies length of segment
(e.g. v_germline_end)</dd>
<dt>germ_aa_start</dt>
<dd>Column name of index of segment start within germline 
segment in AA (if amino_acid=TRUE, e.g. v_germline_start)</dd>
<dt>germ_aa_length</dt>
<dd>Similar to germ_start, but specifies length of segment
in AA (if amino_acid=TRUE, e.g. v_germline_end)</dd>
<dt>amino_acid</dt>
<dd>Perform reconstruction on amino acid sequence (experimental)</dd></dl>

Arguments

getGermline get germline segment from specified receptor and segment — getGermline

<dl>

<dt>receptor</dt>
<dd>row from AIRR-table containing sequence of interest</dd>


<dt>references</dt>
<dd>list of reference segments. Must be specific to
locus and segment</dd>


<dt>segment</dt>
<dd>Gene segment to search. Must be V, D, or J.</dd>


<dt>field</dt>
<dd>Column name for segment gene call (e.g. v_call)</dd>


<dt>germ_start</dt>
<dd>Column name of index of segment start within germline 
segment (e.g. v_germline_start)</dd>


<dt>germ_end</dt>
<dd>Similar to germ_start, but specifies end of segment 
(e.g. v_germline_end)</dd>


<dt>germ_length</dt>
<dd>Similar to germ_start, but specifies length of segment
(e.g. v_germline_end)</dd>


<dt>germ_aa_start</dt>
<dd>Column name of index of segment start within germline 
segment in AA (if amino_acid=TRUE, e.g. v_germline_start)</dd>


<dt>germ_aa_length</dt>
<dd>Similar to germ_start, but specifies length of segment
in AA (if amino_acid=TRUE, e.g. v_germline_end)</dd>


<dt>amino_acid</dt>
<dd>Perform reconstruction on amino acid sequence (experimental)</dd>

</dl>

getGermline: getGermline get germline segment from specified receptor and segment

Description

Usage

Value

Arguments