Permutation Based QQ Plot and Inflation Factor Estimation

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Documentation for package ‘QQperm’ version 1.0.1

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QQperm-package QQperm: A package for permutation-based QQ plots and inflation factor estimates.
estlambda2 Estimate the inflation factor for a distribution of observed P-values or 1-df chi-square test.
example.data An example collapsing data matrix and the associated case/control status
example.Ps Distributions of expected and observed P-values from the igm.data dataset.
igm.get.pvalues The permutation-based empirical NULL distribution of P-values is generated through label switching and permutation of the true case/control assignment. To achieve this, for a given matrix it randomly permutes the case and control labels of the original configuration and then recomputes the two-tail Fisher's Exact test for all genes. This is repeated n.permutation (e.g., 1000) times. For each of the n.permutations the p-values are ordered and then the mean of each rank-ordered estimate is taken across the n.permutations, i.e., the average 1st order statistic, the average 2nd order statistic, etc. These then represent the empirical estimates of the expected ordered p-values (expected -log10(p-values)). This empirical-based expected p-value distribution no longer depends on an assumption that the p-values are uniformly distributed under the null.
igm.read.data Read sample file and genotype collapsing matrix in IGM (Insitute for Genomic Medicine, Columbia University) format.
QQperm QQperm: A package for permutation-based QQ plots and inflation factor estimates.
qqperm QQperm: A package for permutation-based QQ plots and inflation factor estimates.
qqplot QQ plot of observed P-values vs expected P-values, using the empirical (permutation-based) expected p-value distribution. This empirical-based expected p-value distribution no longer depends on an assumption that the Fisher's Exact two-tailed p-values are uniformly distributed under the null. For a given matrix, the permutation-based expected distribution is plotted relative to the observed order statistic to get the permutation-based QQ plot.
toy.data An example collapsing data matrix and the associated case/control status