readIgFasta

<code>readIgFasta</code> reads a fasta-formatted file of immunoglobulin (Ig)
sequences and returns a named vector of those 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

readIgFasta function

<dl><dt>fasta_file</dt>
<dd>fasta-formatted file of immunoglobulin sequences.</dd>
<dt>strip_down_name</dt>
<dd>if <code>TRUE</code>, will extract only the allele name
from the strings fasta file's sequence names.</dd>
<dt>force_caps</dt>
<dd>if <code>TRUE</code>, will force nucleotides to
uppercase.</dd></dl>

Arguments

Read immunoglobulin sequences — readIgFasta

<dl>

<dt>fasta_file</dt>
<dd>fasta-formatted file of immunoglobulin sequences.</dd>


<dt>strip_down_name</dt>
<dd>if <code>TRUE</code>, will extract only the allele name
from the strings fasta file's sequence names.</dd>


<dt>force_caps</dt>
<dd>if <code>TRUE</code>, will force nucleotides to
uppercase.</dd>

</dl>

readIgFasta: Read immunoglobulin sequences

Description

Usage

Value

Arguments

See Also

Examples