snprelate_ld_select

The tagged snp set is (by sliding window) representative and strongly not
redundant.

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_ld_select function

<dl><dt>gdata</dt>
<dd>A GenotypeData object</dd>
<dt>window_length</dt>
<dd>Max length in kb of the window</dd>
<dt>min_r2</dt>
<dd>Minimum r2 value to report</dd>
<dt>window_size</dt>
<dd>Max number of SNPs in LD window</dd>
<dt>snps_idx</dt>
<dd>Indices of snps to use</dd>
<dt>scans_idx</dt>
<dd>Indices of scans to use</dd>
<dt>remove.monosnp</dt>
<dd>if TRUE, remove monomorphic SNPs</dd>
<dt>autosome.only</dt>
<dd>if <code>TRUE</code>, use autosomal SNPs only; if it is a
 numeric or character value, keep SNPs according to the specified
 chromosome</dd>
<dt>method</dt>
<dd>"composite", "r", "dprime", "corr", see details</dd>
<dt>threads</dt>
<dd>The number of threads to use, currently ignored</dd>
<dt>quiet</dt>
<dd>Whether to be quiet</dd>
<dt>...</dt>
<dd>Forwarded to SNPRelate::snpgdsLDpruning</dd></dl>

Arguments

Wrapper for snpgdsLDpruning to select Tag SNPs — snprelate_ld_select

<dl>

<dt>gdata</dt>
<dd>A GenotypeData object</dd>


<dt>window_length</dt>
<dd>Max length in kb of the window</dd>


<dt>min_r2</dt>
<dd>Minimum r2 value to report</dd>


<dt>window_size</dt>
<dd>Max number of SNPs in LD window</dd>


<dt>snps_idx</dt>
<dd>Indices of snps to use</dd>


<dt>scans_idx</dt>
<dd>Indices of scans to use</dd>


<dt>remove.monosnp</dt>
<dd>if TRUE, remove monomorphic SNPs</dd>


<dt>autosome.only</dt>
<dd>if <code>TRUE</code>, use autosomal SNPs only; if it is a
 numeric or character value, keep SNPs according to the specified
 chromosome</dd>


<dt>method</dt>
<dd>"composite", "r", "dprime", "corr", see details</dd>


<dt>threads</dt>
<dd>The number of threads to use, currently ignored</dd>


<dt>quiet</dt>
<dd>Whether to be quiet</dd>


<dt>...</dt>
<dd>Forwarded to SNPRelate::snpgdsLDpruning</dd>

</dl>

snprelate_ld_select: Wrapper for snpgdsLDpruning to select Tag SNPs

Description

Usage

Value

Arguments