QQperm: Permutation Based QQ Plot and Inflation Factor Estimation

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Provides users the necessary utility functions to generate permutation-based QQ plots and also estimate inflation factor based on the empirical NULL distribution. While it has general utility, it is particularly helpful when the skewness of the Fisher's Exact test in sparse data situations with imbalanced case-control sample sizes renders the reliance on the uniform chi-square expected distribution inappropriate.

Author
Slave Petrovski and Quanli Wang
Date of publication
2016-10-09 09:15:16
Maintainer
Quanli Wang <quanli@stat.duke.edu>
License
GPL (>= 2)
Version
1.0.1

View on CRAN

Man pages

estlambda2
Estimate the inflation factor for a distribution of observed...
example.data
An example collapsing data matrix and the associated...
example.Ps
Distributions of expected and observed P-values from the...
igm.get.pvalues
The permutation-based empirical NULL distribution of P-values...
igm.read.data
Read sample file and genotype collapsing matrix in IGM...
QQperm
QQperm: A package for permutation-based QQ plots and...
qqplot
QQ plot of observed P-values vs expected P-values, using the...
toy.data
An example collapsing data matrix and the associated...

Files in this package

QQperm
QQperm/NAMESPACE
QQperm/demo
QQperm/demo/example.R
QQperm/demo/00Index
QQperm/data
QQperm/data/example.Ps.RData
QQperm/data/toy.data.RData
QQperm/data/example.data.RData
QQperm/R
QQperm/R/IGM.R
QQperm/R/data.R
QQperm/R/QQ.R
QQperm/R/QQperm.R
QQperm/MD5
QQperm/DESCRIPTION
QQperm/man
QQperm/man/QQperm.Rd
QQperm/man/igm.get.pvalues.Rd
QQperm/man/qqplot.Rd
QQperm/man/example.data.Rd
QQperm/man/toy.data.Rd
QQperm/man/igm.read.data.Rd
QQperm/man/example.Ps.Rd
QQperm/man/estlambda2.Rd