Contents

1 Introduction

dn8 format is a representation for GWAS summary statistics developed at Channing Division of Network Medicine.

This package illustrates how to produce informative interactive visualizations for GWAS summary statistics, based on the TnT package in Bioconductor.

2 Example

A main problem is extracting information from archives of GWAS summary statistics. We use an example data frame, gtex_b38_lung_chr20_exc, which has EQTL p-values for a small number of genes on chr20, derived from GTEx results for lung tissue..

suppressPackageStartupMessages({
  library(tnt4dn8)
})
## 16/66 packages newly attached/loaded, see sessionInfo() for details.
data(gtex_b38_lung_chr20_exc)
chk2 = gtex_b38_lung_chr20_exc |> filter_sym("SOX12", radius=5e4) |> as.data.frame()
tntplot(chk2)
##   1662 genes were dropped because they have exons located on both strands
##   of the same reference sequence or on more than one reference sequence,
##   so cannot be represented by a single genomic range.
##   Use 'single.strand.genes.only=FALSE' to get all the genes in a
##   GRangesList object, or use suppressMessages() to suppress this message.

You can use click wheel on a mouse to pan and zoom on this display, and the annotation underneath the manhattan plot will become more detailed.