CalcThreshold: Function to calculate threshold for GWAS

In RAINBOWR: Genome-Wide Association Study with SNP-Set Methods

Function to calculate threshold for GWAS

Description

Calculate thresholds for the given GWAS (genome-wide association studies) result by the Benjamini-Hochberg method or Bonferroni method.

Usage

CalcThreshold(input, sig.level = 0.05, method = "BH")

Arguments

input	Data frame of GWAS results where the first column is the marker names, the second and third column is the chromosome amd map position, and the forth column is -log10(p) for each marker.
sig.level	Significance level for the threshold. The default is 0.05. You can also assign vector of sinificance levels.
method	Two methods are offered: "BH" : Benjamini-Hochberg method. To control FDR, use this method. "Bonf" : Bonferroni method. To perform simple correction of multiple testing, use this method. You can also assign both of them by 'method = c("BH", "Bonf")'

Value

The value of the threshold. If there is no threshold, it returns NA.

References

Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc. 57(1): 289-300.

Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci. 100(16): 9440-9445.

RAINBOWR documentation built on Sept. 12, 2023, 9:08 a.m.