lambda_1000: Normalize Lambda inflation factors to specific case-control...
In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description Usage Arguments Value Author(s) References Examples

Lambda inflation statistics are influenced by the size of the generating datasets. To facilitate comparison to other studies, this function calculates then converts a given lambda from n cases and m controls, to be equivalent to 1000 cases and 1000 controls.

1	lambda_1000(p.values, n = 1000, m = 1000)

`p.values`	numeric, a vector of analysis p.values, generated from n cases and m controls (although order switching n/m makes no difference to this function)
`n`	integer, original number of cases that p.values were derived from
`m`	integer, original number of controls that p.values were derived from

A normalized Lambda coefficient

Nicholas Cooper nick.cooper@cimr.cam.ac.uk

Freedman M.L., et al. Assessing the impact of population stratification on genetic association studies. Nat. Genet. 2004;36:388-393.

# create some p-values with clear 'inflation' (divergence from uniform[0,1])
p.vec <- c(runif(3000)/200,runif(7000)) 
# let's imagine these p values come from 3000 cases and 5000 controls
L1000_a <- lambda_1000(p.vec,3000,5000)
# alternatively, imagine the sample sizes are 10 times larger
L1000_b <- lambda_1000(p.vec,30000,50000)
plot(sort(p.vec),type="l") 
L1000_a; L1000_b