snprelate_qc

Quality control using SNPRelate functions.

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.

Thomas Charlon

snplinkage

Single Nucleotide Polymorphisms Linkage Disequilibrium
Visualizations

Karl Forner

Alessandro Di Cara

Jérôme Wojcik

snprelate_qc function

<dl><dt>gdata</dt>
<dd>Genotype data object</dd>
<dt>samples_nas</dt>
<dd>NA threshold for samples, default 3 pct</dd>
<dt>ibs</dt>
<dd>Samples identity by state threshold, default 99 pct</dd>
<dt>keep_ids</dt>
<dd>Samples ids to keep even if IBS is higher than threshold.
Used for monozygotic twins.</dd>
<dt>snps_nas</dt>
<dd>NA threshold for SNPs, default 1 pct</dd>
<dt>maf</dt>
<dd>Minor allele frequency threshold, default 5 pct</dd>
<dt>tagsnp</dt>
<dd>TagSNP r2 correlation threshold, default 0.8</dd>
<dt>n_cores</dt>
<dd>Number of cores</dd></dl>

Arguments

snprelate_qc — snprelate_qc

<dl>

<dt>gdata</dt>
<dd>Genotype data object</dd>


<dt>samples_nas</dt>
<dd>NA threshold for samples, default 3 pct</dd>


<dt>ibs</dt>
<dd>Samples identity by state threshold, default 99 pct</dd>


<dt>keep_ids</dt>
<dd>Samples ids to keep even if IBS is higher than threshold.
Used for monozygotic twins.</dd>


<dt>snps_nas</dt>
<dd>NA threshold for SNPs, default 1 pct</dd>


<dt>maf</dt>
<dd>Minor allele frequency threshold, default 5 pct</dd>


<dt>tagsnp</dt>
<dd>TagSNP r2 correlation threshold, default 0.8</dd>


<dt>n_cores</dt>
<dd>Number of cores</dd>

</dl>

snprelate_qc: snprelate_qc

Description

Usage

Value

Arguments

Examples