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1. R installed in the system
2. Disease A case and control sample sizes.
3. List of disease B associated loci (risk allele frequencies, and odds ratios)
The file includes one R function. You can read the file with "source" command and run the get.power function. The function arguments are as follows,
## ARGUMENTS ######################################################### ## nexp: number of simulation experiments to measure power (e.g 1000) ## N: case sample size ## Ncont: control sample size (New: 7/14/15) ## p: number of SNPs ## rafs: risk allele frequency ## ORs: true odds ratios for generative model ## ORs.for.method: odds ratios that the method "think" are true ## phi: proportion of contaminating group ## thres: p-value threshold (can be vector, for examining multiple different thresholds.)
PowerBUHMBOX | Power of BUHMBOX |
PowerUnweighted | Power if we ignore the weighting based on OR and RAF |
PowerNondirectional | Power if we combine correlations using Jennrich's chi-square-like style, which ignores the directions of z-scores |
Threshold | Significance threshold |
Nexp | Number of repeats for power calculation |
N | Case sample size |
Ncont | Control sample size |
NSNP | Number of SNPs used. |
Pi | Heterogeneity proportion. |