gtable_ld_associations

Creates a gtable of a linkage disequilibrium, chromosomic positions, and
association scores ggplots.

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

gtable_ld_associations function

<dl><dt>df_assocs</dt>
<dd>SNP annotation data frame with columns chromosome,
position, and as specified by parameters pvalue_colname
and optionally labels_colname.</dd>
<dt>df_ld</dt>
<dd>Data frame with columns SNP_A, SNP_B, and R2, as
returned by the snprelate_ld function.</dd>
<dt>pvalue_colname</dt>
<dd>Column name of df_snp with association values</dd>
<dt>labels_colname</dt>
<dd>Optional column name of df_snp with labels.
Set NULL to remove labels.</dd>
<dt>n_labels</dt>
<dd>Number of labels of most associated SNPs to display.</dd>
<dt>diamonds</dt>
<dd>Should the values be displayed as diamonds or points ?
Default is TRUE for up to 40 SNPs.</dd>
<dt>linked_area</dt>
<dd>Add a linked area to associations points.
Default same as diamonds.</dd>
<dt>point_size</dt>
<dd>Point size for ggplot_ld, ignored if diamonds is TRUE.</dd>
<dt>colors</dt>
<dd>Colors of SNPs</dd>
<dt>...</dt>
<dd>Passed to ggplot_associations</dd></dl>

Arguments

Gtable of linkage disequilibrium and associations — gtable_ld_associations

<dl>

<dt>df_assocs</dt>
<dd>SNP annotation data frame with columns chromosome,
position, and as specified by parameters pvalue_colname
and optionally labels_colname.</dd>


<dt>df_ld</dt>
<dd>Data frame with columns SNP_A, SNP_B, and R2, as
returned by the snprelate_ld function.</dd>


<dt>pvalue_colname</dt>
<dd>Column name of df_snp with association values</dd>


<dt>labels_colname</dt>
<dd>Optional column name of df_snp with labels.
Set NULL to remove labels.</dd>


<dt>n_labels</dt>
<dd>Number of labels of most associated SNPs to display.</dd>


<dt>diamonds</dt>
<dd>Should the values be displayed as diamonds or points ?
Default is TRUE for up to 40 SNPs.</dd>


<dt>linked_area</dt>
<dd>Add a linked area to associations points.
Default same as diamonds.</dd>


<dt>point_size</dt>
<dd>Point size for ggplot_ld, ignored if diamonds is TRUE.</dd>


<dt>colors</dt>
<dd>Colors of SNPs</dd>


<dt>...</dt>
<dd>Passed to ggplot_associations</dd>

</dl>

gtable_ld_associations: Gtable of linkage disequilibrium and associations

Description

Usage

Value

Arguments