BUHMBOX Power calculation manual

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Prerequisite

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)

How to run

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.)
rafs, ORs, ORs.for.method will be repeated as necessary for p SNPs. That is, if you want to use OR of 1.2 for all SNPs, you can just put 1.2.

Output

In our output dataframe:
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.
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