HapMap

A dataset containing a subset of the draft release 2 for genome-wide SNP
genotyping in DNA samples from 11 human populations (sometimes referred to as
the "HapMap 3" samples). Only the PLINK .map file was used. Approximately
2.5% of the SNPs in each chromosome were retained. The p-values, zscores,
and effectsizes were simulated using random distributions in R. Annotation
information (nearest gene and distance to nearest gene) was obtained from the
UCSC genome annotation database for the Mar. 2006 GenBank freeze assembled by
NCBI (hg18, Build 36.1)

datasets

Create interactive manhattan, Q-Q and volcano plots that are usable from the R console,
in 'Dash' apps, 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 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'

HapMap function

A data frame with 14412 rows and 8 variables:<dl class="dl-horizontal">
 <dt>CHR</dt><dd>chromosome number. Autosomes coded 1 through 22, and 23 is the X
 chromosome (<code>integer</code>)</dd> <dt>BP</dt><dd>genomic base-pair position
 (<code>integer</code>)</dd> <dt>P</dt><dd>p-value (<code>numeric</code>)</dd> <dt>SNP</dt><dd>rs# or snp
 identifier (<code>character</code>)</dd> <dt>ZSCORE</dt><dd>z-score (<code>numeric</code>)</dd>
 <dt>EFFECTSIZE</dt><dd>effect size (<code>numeric</code>)</dd> <dt>GENE</dt><dd>nearest gene to
 the SNP (<code>character</code>)</dd> <dt>DISTANCE</dt><dd>distance between the SNP and
 GENE. if <code>DISTANCE=0</code> then the SNP is located in the GENE
 (<code>integer</code>)</dd> </dl>

Format

Subset of HapMap data with simulated GWAS results — HapMap

A data frame with 14412 rows and 8 variables:<dl class='dl-horizontal'>
 <dt>CHR</dt><dd>chromosome number. Autosomes coded 1 through 22, and 23 is the X
 chromosome (<code>integer</code>)</dd> <dt>BP</dt><dd>genomic base-pair position
 (<code>integer</code>)</dd> <dt>P</dt><dd>p-value (<code>numeric</code>)</dd> <dt>SNP</dt><dd>rs# or snp
 identifier (<code>character</code>)</dd> <dt>ZSCORE</dt><dd>z-score (<code>numeric</code>)</dd>
 <dt>EFFECTSIZE</dt><dd>effect size (<code>numeric</code>)</dd> <dt>GENE</dt><dd>nearest gene to
 the SNP (<code>character</code>)</dd> <dt>DISTANCE</dt><dd>distance between the SNP and
 GENE. if <code>DISTANCE=0</code> then the SNP is located in the GENE
 (<code>integer</code>)</dd> </dl>

HapMap: Subset of HapMap data with simulated GWAS results

Description

Usage

Arguments

Format