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Calculating Genomic Inflation Factor

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

gwas plink
• 43,332 views • link
updated by GabrielMontenegro GabrielMontenegro • written by Debs • Debs

3 answers

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
• 3 views • link
updated by zx8754 zx8754 • written by 1234Jc4321 1234Jc4321

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
• 0 views • link
updated by zx8754 zx8754 • written by aydzhouyuan • aydzhouyuan

Or using GenABEL in R:

library("GenABEL")

estlambda(Pvalues, method="median")
• 0 views • link
written by GabrielMontenegro GabrielMontenegro

Package ‘GenABEL’ was removed from the CRAN repository.

• 1 views • link
written by zx8754 zx8754

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