| CalcThreshold {RAINBOWR} | R Documentation |
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 |
Three 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. "Sidak": Sidak method. You can also assign two 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.