utils

GenerateLookup

CalRiskScore

FuncForCompHaplo

na_to_empty_string

GenerateLookup() called in CalEpletMHCII()

A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.

Joan Zhang

hlaR

Tools for HLA Data

Aileen Johnson

Christian P Larsen

utils function

<dl><dt>lkup_in</dt>
<dd>data table</dd>
<dt>locus_in</dt>
<dd>string
CalRiskScore() calculate DR DQ risk score, it's called in CalEpletMHCII()</dd>
<dt>dat_in</dt>
<dd>dataframe
FuncForCompHaplo() called in ImputeHaplo()</dd>
<dt>tbl_raw</dt>
<dd>data frame</dd>
<dt>tbl_in</dt>
<dd>data frame
na_to_empty_string()</dd>
<dt>df</dt>
<dd>dataframe</dd></dl>

Arguments

Basic functions — utils

<dl>

<dt>lkup_in</dt>
<dd>data table</dd>


<dt>locus_in</dt>
<dd>string
CalRiskScore() calculate DR DQ risk score, it's called in CalEpletMHCII()</dd>


<dt>dat_in</dt>
<dd>dataframe
FuncForCompHaplo() called in ImputeHaplo()</dd>


<dt>tbl_raw</dt>
<dd>data frame</dd>


<dt>tbl_in</dt>
<dd>data frame
na_to_empty_string()</dd>


<dt>df</dt>
<dd>dataframe</dd>

</dl>

utils: Basic functions

Description

Usage

Arguments