chisq_pvalues_gdata

Compute Chi-squared p-values on a 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

chisq_pvalues_gdata function

<dl><dt>gdata</dt>
<dd>Genotype data object</dd>
<dt>snp_idxs</dt>
<dd>SNPs indexes</dd>
<dt>response_column</dt>
<dd>Response column in gdata scans annotations data frame</dd>
<dt>response_value</dt>
<dd>Response value. The response vector will be a logical,
true if equal to the value, false otherwise.</dd>
<dt>threshold</dt>
<dd>Keep only associations greater than the threshold</dd>
<dt>...</dt>
<dd>Passed to chisq_pvalues</dd></dl>

Arguments

Compute Chi-squared p-values on a Genotype data object — chisq_pvalues_gdata

<dl>

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


<dt>snp_idxs</dt>
<dd>SNPs indexes</dd>


<dt>response_column</dt>
<dd>Response column in gdata scans annotations data frame</dd>


<dt>response_value</dt>
<dd>Response value. The response vector will be a logical,
true if equal to the value, false otherwise.</dd>


<dt>threshold</dt>
<dd>Keep only associations greater than the threshold</dd>


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

</dl>

chisq_pvalues_gdata: Compute Chi-squared p-values on a Genotype data object

Description

Usage

Value

Arguments