Package 'TrumpetPlots'

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)

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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)

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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

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