significantSNP

SNP rs identifiers from <code><a rd-options="" href="/link/HapMap?package=manhattanly&version=0.2.0" data-mini-rdoc="manhattanly::HapMap">HapMap</a></code> dataset that are significant at <code>p-value
&lt; 1e-6</code>

datasets

Create interactive Q-Q, manhattan and volcano plots that are usable from the R console,
in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps.
Hover the mouse pointer over a point to show details or drag a rectangle to
zoom. A manhattan plot is a popular graphical method for visualizing results
from high-dimensional data analysis such as a (epi)genome wide association study
(GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter
plot against their genomic position. Manhattan plots are used for visualizing
potential regions of interest in the genome that are associated with a phenotype.
Interactive manhattan plots allow the inspection of specific value (e.g. rs number or
gene name) by hovering the mouse over a cell, as well as zooming into a region of the
genome (e.g. a chromosome) by dragging a rectangle around the relevant area.
This work is based on the 'qqman' package by Stephen Turner and the 'plotly.js'
engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq'
functions in the 'qqman' package, with the advantage of including extra annotation
information and interactive web-based visualizations directly from R.
Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them)
can be viewed and modified in a web browser.

Sahir Bhatnagar

manhattanly

Interactive Q-Q and Manhattan Plots Using 'plotly.js'

significantSNP function

A character vector with 20 elements

Format

SNP rs identifiers from <code><a rd-options='' href='HapMap'>HapMap</a></code> dataset that are significant at <code>p-value
&lt; 1e-6</code>

significantSNP: Character vector of SNPs to highlight

Description

Usage

Arguments

Format

See Also