QQperm                  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.Ps              Distributions of expected and observed P-values
                        from the igm.data dataset.
example.data            An example collapsing data matrix and the
                        associated case/control status
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.
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
