LCT.EUR.b37

LCT.EUR.b37.fam

LCT.EUR.b37.bed

LCT.EUR.b38

LCT.EUR.b38.fam

LCT.EUR.b38.bed

These data contain the genotype matrix from the 1000 Genomes EUR ancestry individuals in the Lactase gene (positions retrieved from GeneCards. 
 Information about individuals is present in <code>LCT.EUR.b37/b38.fam</code>, including the subpopulation, in a format needed to generate a bedmatrix. 
 Two set of files are available: one set in build 37, and one set in build 38. 
 Data have been anonymized by randomly sampling the genotype positions.

LCT.EUR

Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome using the RAVA-FIRST approach (Bocher et al. 2022 <doi:10.1371/journal.pgen.1009923>). Ravages also enables to perform genetic simulations (Bocher et al. 2023 <doi:10.1002/gepi.22529>).

Ozvan Bocher

Ravages

Rare Variant Analysis and Genetic Simulations

Hervé Perdry

Gaelle Marenne

LCT.EUR function

<dl>
 <dt><code>LCT.EUR.b37/b38.bed</code></dt>
<dd>Binary genotype file</dd> <dt><code>LCT.EUR.b37/b38.bim</code></dt>
<dd>Variant information file</dd> <dt><code>LCT.EUR.b37/b38.fam</code></dt>
<dd>Sample information file</dd> 
</dl>

Format

LCT genotypes matrix — LCT.EUR

<dl>
 <dt><code>LCT.EUR.b37/b38.bed</code></dt>
<dd>Binary genotype file</dd>

 <dt><code>LCT.EUR.b37/b38.bim</code></dt>
<dd>Variant information file</dd>

 <dt><code>LCT.EUR.b37/b38.fam</code></dt>
<dd>Sample information file</dd>

 
</dl>

LCT genotypes matrix

LCT.EUR: LCT genotypes matrix

Description

Arguments

Format

References

Examples