print_qc_as_tex_table

Print information about quality control performed by the snprelate_qc
function.

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

print_qc_as_tex_table function

<dl><dt>gdata_qc</dt>
<dd>Genotype Data object object returned by snprelate_qc</dd>
<dt>label</dt>
<dd>Label of the Tex table</dd>
<dt>caption</dt>
<dd>Caption of the Tex table</dd></dl>

Arguments

print_qc_as_tex_table — print_qc_as_tex_table

<dl>

<dt>gdata_qc</dt>
<dd>Genotype Data object object returned by snprelate_qc</dd>


<dt>label</dt>
<dd>Label of the Tex table</dd>


<dt>caption</dt>
<dd>Caption of the Tex table</dd>

</dl>

print_qc_as_tex_table: print_qc_as_tex_table

Description

Usage

Value

Arguments