plotCcLocusMultiBySampleSize: Tests the power to detect a gene locus (i.e. locus defined by...

In stephansanders/wgsPowerTest: Whole Genome Sequencing Power Calculations

Description

Tests the power to detect a gene locus (i.e. locus defined by a gene rather than variant) using case control data varying sample size.

Usage

plotCcLocusMultiBySampleSize(R, N, r = 1, s, f_gene, f, K, AF_bar, N_rep,
  p_thres_cc_locus_multi = 0.05, name = "Test", col = "#e41a1c")

Arguments

R	Relative risk (numeric).
N	Maximum sample size (integer).
r	Case:Control ratio (numeric).
s	Number of possible rare variants per gene (numeric).
f_gene	Number of possible functional rare variants per gene (numeric).
f	Proportion of functional rare variants that mediate risk for the disorder (numeric, 0-1).
K	Prevalence of the disorder (numeric, 0-1).
AF_bar	Average minor allele frequency (numeric, 0-1).
N_rep	Number of replicate simulations (integer).
p_thres_cc_locus_multi	p-value threshold after correction for multiple comparisons (numeric, 0-1).
name	Prefix for plot filenames (text).
col	Color of the line (hex).

Value

A PDF showing the estimated statistical power as the sample size is varied.

Examples

R <- 2.5
N <- 20000
r <- 1
s <- 615
f_gene <- 123
f <- 0.2
K <- 0.01
AF_bar <- 0.001
N_rep <- 50
p_thres_cc_locus_multi <- 0.05 / 20000
name <- "Test1"
col <- "#e41a1c"
plotCcLocusMultiBySampleSize()

stephansanders/wgsPowerTest documentation built on May 4, 2019, 1:23 p.m.