Calculating Genomic Inflation Factor

Question

[Debs]

Hi All,

Since I had a huge genetic data set, I divided it into 22 chunks (1 for each chromosome) and ran a logistic regression (case-control phenotype) adjusting for three covariates on each of the chunks. I have the PLINK outputs i.e. the assoc.logistic and assoc.logistic.adjusted files.

How do I calculate the genomic inflation factor for the entire dataset?

Thanks,

Debs

[Zev.Kronenberg]

Wiki has an explanation on how to find the estimation of lambda

http://en.wikipedia.org/wiki/Population_stratification

[zx8754]

Related posts:

• Compute confidence intervals for lambda genomic factor statistics

• https://stats.stackexchange.com/questions/110755/how-calculate-inflation-observed-and-expected-p-values-from-uniform-distribution

Answer 1

[1234Jc4321]

Plink calculates the genomic inflation factor:

plink --bfile hapmap1 --assoc --adjust --out as2

When the --adjust command is used, the log file records the inflation factor calculated for the genomic control analysis, and the mean chi-squared statistic (that should be 1 under the null):

Genomic inflation factor (based on median chi-squared) is 1.18739
Mean chi-squared statistic is 1.14813

If it is possible, you will have to merge all your files together before.

plink --file fA --merge-list allfiles.txt --make-bed --out mynewdata

Answer 2

[aydzhouyuan]

Hope this would be help:

## Reads data
S <- read.table(input, header = FALSE)

if (stat_type == "Z")
   z = S[, 1]

if (stat_type == "CHISQ")
   z = sqrt(S[, 1])

if (stat_type == "PVAL")
   z = qnorm(S[, 1] / 2)

## calculates lambda
lambda = round(median(z^2) / 0.454, 3)

lambda

[Kevin Blighe]

You should state from where 0.454 derives, i.e.:

qchisq(0.5, 1)
[1] 0.4549364

Actually, rounded up, it equates to 0.455

See my previous answer: Compute confidence intervals for lambda genomic factor statistics

Answer 3

[GabrielMontenegro]

Or using GenABEL in R:

library("GenABEL")

estlambda(Pvalues, method="median")

[zx8754]

Package ‘GenABEL’ was removed from the CRAN repository.