gdata_add_gene_annots

Add biomaRt gene annotations to Genotype Data object.

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

gdata_add_gene_annots function

<dl><dt>gdata</dt>
<dd>Genotype Data object</dd>
<dt>snp_idxs</dt>
<dd>SNP indexes</dd>
<dt>rsids_colname</dt>
<dd>Column of SNP annotation data frame with rs identifiers</dd>
<dt>biomart_metadb</dt>
<dd>List with slots snpmart and ensembl, corresponding to 
the biomart databases to query for SNP identifiers
and gene names, respectively. See get_biomart_metadb
function.</dd></dl>

Arguments

gdata_add_gene_annots — gdata_add_gene_annots

<dl>

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


<dt>snp_idxs</dt>
<dd>SNP indexes</dd>


<dt>rsids_colname</dt>
<dd>Column of SNP annotation data frame with rs identifiers</dd>


<dt>biomart_metadb</dt>
<dd>List with slots snpmart and ensembl, corresponding to 
the biomart databases to query for SNP identifiers
and gene names, respectively. See get_biomart_metadb
function.</dd>

</dl>

gdata_add_gene_annots: gdata_add_gene_annots

Description

Usage

Value

Arguments