| Title: | Visualization of Genetic Association Studies |
| Version: | 0.0.1.1 |
| Description: | Visualizes the relationship between allele frequency and effect size in genetic association studies. The input is a data frame containing association results. The output is a plot with the effect size of risk variants in the Y axis, and the allele frequency spectrum in the X axis. Corte et al (2023) <doi:10.1101/2023.04.21.23288923>. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Depends: | R (≥ 2.10), data.table, ggplot2, magrittr, stats, purrr (≥ 1.0.1) |
| LazyData: | true |
| NeedsCompilation: | no |
| Packaged: | 2023-06-13 00:57:06 UTC; garcij62 |
| Author: | Judit García-González
 [aut, cre],
Lathan Liou [ctb] |
| Maintainer: | Judit García-González <judit.garciagonzalez@mssm.edu> |
| Repository: | CRAN |
| Date/Publication: | 2023-06-13 08:50:13 UTC |
Trumpets
Description
This function generates trumpet plots
Usage
plot_trumpets(
dataset = toy_data,
rsID = "rsID",
freq = "freq",
A1_beta = "A1_beta",
Analysis = "Analysis",
Gene = "Gene",
calculate_power = TRUE,
show_power_curves = TRUE,
exist_datapwr = NULL,
threshold = c(0.7, 0.9),
N = 1e+05,
alpha = 5e-08,
Nfreq = 500,
power_color_palette = c("purple", "deeppink"),
analysis_color_palette = c("#018571", "#a6611a")
)
Arguments
dataset |
Input text file with genetic association results. Columns required are rsID, freq, A1_beta, Analysis and Gene. |
rsID |
(required) Single Nucleotide Polymorphism (SNP) name. |
freq |
(required) allele frequency of effect SNP. |
A1_beta |
(required) risk allele effect size. |
Analysis |
(optional) adds colour to the type of analysis (e.g. GWAS, Sequencing). |
Gene |
(optional) Candidate gene name (can be empty). |
calculate_power |
(TRUE/FALSE) Calculate power curves. Choose TRUE to add power curves for a given threshold, alpha, sample size N and number of allele frequencies. Choose FALSE if you already ran powerCurves() outside or do not want to show power curves. |
show_power_curves |
(TRUE/FALSE) Show power curves in plot |
exist_datapwr |
Existing dataframe containing columns: freq, pos.b.for.f, neg.b.for.f, powerline. |
threshold |
Required if power == TRUE. Can be a single number or a vector of statistical power thresholds. |
N |
(Required if calculate_power == TRUE). Sample size used to test the association. |
alpha |
(Required if calculate_power == TRUE). |
Nfreq |
(Required if calculate_power == TRUE). Number of allele frequency data points generated to calculate the power curves. We recommend Nfreq>1000 for power curves with high resolution. Note that this will slow down the rendering of the plot. |
power_color_palette |
A vector of colours for the power curves. Number of colors should match number of thresholds supplied. |
analysis_color_palette |
A vector of colours for the analysis types. |
Value
Creates a Trumpet plot with variant allele frequency (X axis, log10 scale) and effect size information (Y axis).
Examples
plot_trumpets(dataset = toy_data)
Power Curves for Trumpet Plots
Description
This function generates curves indicating statistical power in Trumpet plots
Usage
powerCurves(threshold = 0.8, N = 4e+05, alpha = 5e-08, Nfreq = 500)
Arguments
threshold |
user-specified power level |
N |
sample size |
alpha |
significance threshold |
Nfreq |
Number of allele frequency data points generated to calculate the power curves |
Value
A data frame with the power estimated for each allele frequency and effect size, given a: Statistical power threshold, significance threshold (alpha value), and sample size
Examples
powerCurves(threshold = 0.8, N=400000, alpha = 5e-8)
Toy dataset
Description
A data frame with 9999 genetic associations
Usage
data(toy_data)
Format
A data frame with 9999 genetic associations
Details
rsID. SNP name
freq. allele frequency of effect SNP
A1_beta. effect size
Analysis. adds colour to the type of analysis (e.g. GWAS, Sequencing)
Gene. Candidate gene name
N.
trait. ToyDataPheno