In stephansanders/wgsPowerTest: Whole Genome Sequencing Power Calculations
Install the wgsPowerCalc project in R:
devtools::install_github("stephansanders/wgsPowerTest")
library(wgsPowerCalc)
Set the working directory for where you want the PDFs to be printed
setwd("/path/to/directory/")
Figure S2A - De novo cohort, burden analysis, varying sample size
Note that multiple PDFs can be placed into Adobe Illustrator together (drag and drop) to combine multiple lines.
# These values are constant for all seven analyses
p_thres_denovo_burden <- 0.05 / 1000 # p-value threshold (1000 hypotheses)
R <- 5 # Maximum relative risk
N <- 20000 # Sample size
r <- 1 # Case:Control ratio
# 500 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=25*0.0996, f=0.05/25, p_thres_denovo_burden, name="FigS2A_500", col="#a65628")
# 200 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=10*0.0996, f=0.05/10, p_thres_denovo_burden, name="FigS2A_200", col="#ffff33")
# 100 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=5*0.0996, f=0.05/5, p_thres_denovo_burden, name="FigS2A_100", col="#ff7f00")
# 50 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=2.5*0.0996, f=0.05/2.5, p_thres_denovo_burden, name="FigS2A_50", col="#984ea3")
# 20 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=1*0.0996, f=0.05/1, p_thres_denovo_burden, name="FigS2A_20", col="#4daf4a")
# 10 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=0.5*0.0996, f=0.05/0.5, p_thres_denovo_burden, name="FigS2A_10", col="#377eb8")
# 5 non-risk variants to 1 risk variants
plotDnBurdenBySampleSize(R, N, r, q=0.25*0.0996, f=0.05/0.25, p_thres_denovo_burden, name="FigS2A_5", col="#e41a1c")
Figure S2B - Case control cohort, burden analysis, varying sample size
# These values are constant for all seven analyses
p_thres_cc_burden <- 0.05 / 1000 # p-value threshold (1000 hypotheses)
R <- 1.2 # Maximum relative risk
N <- 200000 # Sample size
r <- 1 # Case:Control ratio
# 500 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=25*5.04, f=0.05/25, p_thres_cc_burden, name="FigS2B_500", col="#a65628")
# 200 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=10*5.04, f=0.05/10, p_thres_cc_burden, name="FigS2B_200", col="#ffff33")
# 100 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=5*5.04, f=0.05/5, p_thres_cc_burden, name="FigS2B_100", col="#ff7f00")
# 50 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=2.5*5.04, f=0.05/2.5, p_thres_cc_burden, name="FigS2B_50", col="#984ea3")
# 20 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=1*5.04, f=0.05/1, p_thres_cc_burden, name="FigS2B_20", col="#4daf4a")
# 10 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=0.5*5.04, f=0.05/0.5, p_thres_cc_burden, name="FigS2B_10", col="#377eb8")
# 5 non-risk variants to 1 risk variants
plotCcBurdenBySampleSize(R, N, r, q=0.25*5.04, f=0.05/0.25, p_thres_cc_burden, name="FigS2B_5", col="#e41a1c")
Figure S2C - De novo cohort, locus analysis, varying sample size
# These values are constant for all seven analyses
p_thres_denovo_locus <- 0.05 / 20000 # p-value threshold (20000 genes)
R <- 5 # Maximum relative risk
N <- 20000 # Sample size
r <- 1 # Case:Control ratio
# 500 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=25*0.0996, f=0.05/25, p_thres_denovo_locus, name="FigS2C_500", col="#a65628")
# 200 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=10*0.0996, f=0.05/10, p_thres_denovo_locus, name="FigS2C_200", col="#ffff33")
# 100 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=5*0.0996, f=0.05/5, p_thres_denovo_locus, name="FigS2C_100", col="#ff7f00")
# 50 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=2.5*0.0996, f=0.05/2.5, p_thres_denovo_locus, name="FigS2C_50", col="#984ea3")
# 20 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=1*0.0996, f=0.05/1, p_thres_denovo_locus, name="FigS2C_20", col="#4daf4a")
# 10 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=0.5*0.0996, f=0.05/0.5, p_thres_denovo_locus, name="FigS2C_10", col="#377eb8")
# 5 non-risk variants to 1 risk variants
plotDnLocusBySampleSize(R, N, r, q=0.25*0.0996, f=0.05/0.25, p_thres_denovo_locus, name="FigS2C_5", col="#e41a1c")
Figure S2D - Case control cohort, locus analysis, varying sample size
# These values are constant for all seven analyses
p_thres_cc_locus_single <- 0.05 / 3000000000 # p-value threshold (3000000000 nucloetides in genome)
R <- 1.2 # Maximum relative risk
N <- 200000 # Sample size
r <- 1 # Case:Control ratio
f_gene <- 123 # Number of possible functional rare variants per gene
K <- 0.01 # Prevalence
AF_bar <- 0.001 # Average rare variant minor allele frequency
N_rep <- 500 # Number of replications (increase for weakly powered analyses)
# 500 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=25*20*f_gene, f_gene, f=0.05/25, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_500", col="#a65628")
# 200 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=10*20*f_gene, f_gene, f=0.05/10, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_200", col="#ffff33")
# 100 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=5*20*f_gene, f_gene, f=0.05/5, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_100", col="#ff7f00")
# 50 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=2.5*20*f_gene, f_gene, f=0.05/2.5, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_50", col="#984ea3")
# 20 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=1*20*f_gene, f_gene, f=0.05/1, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_20", col="#4daf4a")
# 10 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=0.5*20*f_gene, f_gene, f=0.05/0.5, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_10", col="#377eb8")
# 5 non-risk variants to 1 risk variants
plotCcLocusSingleBySampleSize(R, N, r, s=0.25*20*f_gene, f_gene, f=0.05/0.25, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_5", col="#e41a1c")
stephansanders/wgsPowerTest documentation built on May 4, 2019, 1:23 p.m.
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Install the wgsPowerCalc project in R:
devtools::install_github("stephansanders/wgsPowerTest") library(wgsPowerCalc)
Set the working directory for where you want the PDFs to be printed
setwd("/path/to/directory/")
Figure S2A - De novo cohort, burden analysis, varying sample size
Note that multiple PDFs can be placed into Adobe Illustrator together (drag and drop) to combine multiple lines.
# These values are constant for all seven analyses p_thres_denovo_burden <- 0.05 / 1000 # p-value threshold (1000 hypotheses) R <- 5 # Maximum relative risk N <- 20000 # Sample size r <- 1 # Case:Control ratio # 500 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=25*0.0996, f=0.05/25, p_thres_denovo_burden, name="FigS2A_500", col="#a65628") # 200 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=10*0.0996, f=0.05/10, p_thres_denovo_burden, name="FigS2A_200", col="#ffff33") # 100 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=5*0.0996, f=0.05/5, p_thres_denovo_burden, name="FigS2A_100", col="#ff7f00") # 50 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=2.5*0.0996, f=0.05/2.5, p_thres_denovo_burden, name="FigS2A_50", col="#984ea3") # 20 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=1*0.0996, f=0.05/1, p_thres_denovo_burden, name="FigS2A_20", col="#4daf4a") # 10 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=0.5*0.0996, f=0.05/0.5, p_thres_denovo_burden, name="FigS2A_10", col="#377eb8") # 5 non-risk variants to 1 risk variants plotDnBurdenBySampleSize(R, N, r, q=0.25*0.0996, f=0.05/0.25, p_thres_denovo_burden, name="FigS2A_5", col="#e41a1c")
Figure S2B - Case control cohort, burden analysis, varying sample size
# These values are constant for all seven analyses p_thres_cc_burden <- 0.05 / 1000 # p-value threshold (1000 hypotheses) R <- 1.2 # Maximum relative risk N <- 200000 # Sample size r <- 1 # Case:Control ratio # 500 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=25*5.04, f=0.05/25, p_thres_cc_burden, name="FigS2B_500", col="#a65628") # 200 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=10*5.04, f=0.05/10, p_thres_cc_burden, name="FigS2B_200", col="#ffff33") # 100 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=5*5.04, f=0.05/5, p_thres_cc_burden, name="FigS2B_100", col="#ff7f00") # 50 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=2.5*5.04, f=0.05/2.5, p_thres_cc_burden, name="FigS2B_50", col="#984ea3") # 20 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=1*5.04, f=0.05/1, p_thres_cc_burden, name="FigS2B_20", col="#4daf4a") # 10 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=0.5*5.04, f=0.05/0.5, p_thres_cc_burden, name="FigS2B_10", col="#377eb8") # 5 non-risk variants to 1 risk variants plotCcBurdenBySampleSize(R, N, r, q=0.25*5.04, f=0.05/0.25, p_thres_cc_burden, name="FigS2B_5", col="#e41a1c")
Figure S2C - De novo cohort, locus analysis, varying sample size
# These values are constant for all seven analyses p_thres_denovo_locus <- 0.05 / 20000 # p-value threshold (20000 genes) R <- 5 # Maximum relative risk N <- 20000 # Sample size r <- 1 # Case:Control ratio # 500 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=25*0.0996, f=0.05/25, p_thres_denovo_locus, name="FigS2C_500", col="#a65628") # 200 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=10*0.0996, f=0.05/10, p_thres_denovo_locus, name="FigS2C_200", col="#ffff33") # 100 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=5*0.0996, f=0.05/5, p_thres_denovo_locus, name="FigS2C_100", col="#ff7f00") # 50 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=2.5*0.0996, f=0.05/2.5, p_thres_denovo_locus, name="FigS2C_50", col="#984ea3") # 20 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=1*0.0996, f=0.05/1, p_thres_denovo_locus, name="FigS2C_20", col="#4daf4a") # 10 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=0.5*0.0996, f=0.05/0.5, p_thres_denovo_locus, name="FigS2C_10", col="#377eb8") # 5 non-risk variants to 1 risk variants plotDnLocusBySampleSize(R, N, r, q=0.25*0.0996, f=0.05/0.25, p_thres_denovo_locus, name="FigS2C_5", col="#e41a1c")
Figure S2D - Case control cohort, locus analysis, varying sample size
# These values are constant for all seven analyses p_thres_cc_locus_single <- 0.05 / 3000000000 # p-value threshold (3000000000 nucloetides in genome) R <- 1.2 # Maximum relative risk N <- 200000 # Sample size r <- 1 # Case:Control ratio f_gene <- 123 # Number of possible functional rare variants per gene K <- 0.01 # Prevalence AF_bar <- 0.001 # Average rare variant minor allele frequency N_rep <- 500 # Number of replications (increase for weakly powered analyses) # 500 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=25*20*f_gene, f_gene, f=0.05/25, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_500", col="#a65628") # 200 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=10*20*f_gene, f_gene, f=0.05/10, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_200", col="#ffff33") # 100 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=5*20*f_gene, f_gene, f=0.05/5, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_100", col="#ff7f00") # 50 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=2.5*20*f_gene, f_gene, f=0.05/2.5, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_50", col="#984ea3") # 20 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=1*20*f_gene, f_gene, f=0.05/1, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_20", col="#4daf4a") # 10 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=0.5*20*f_gene, f_gene, f=0.05/0.5, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_10", col="#377eb8") # 5 non-risk variants to 1 risk variants plotCcLocusSingleBySampleSize(R, N, r, s=0.25*20*f_gene, f_gene, f=0.05/0.25, K, AF_bar, N_rep, p_thres_cc_locus_single, name="FigS2D_5", col="#e41a1c")
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