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tmp.txt
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tmp.txt
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File A vector of p-values (only necessary input).
π<sub>0</sub> method Either "smoother" or "bootstrap"; the method for automatically choosing tuning parameter in the estimation of π<sub>0</sub>, the proportion of true null hypotheses.
λ range The range of the tuning parameter to estimate π<sub>0</sub>. Must be in [0,1). Optional, see Storey (2002).
λ step size Step size used to determine the number of points between λ range
smooth df Number of degrees-of-freedom to use when estimating π<sub>0</sub> with a smoother. Optional.
π<sub>0</sub> smoother log If TRUE and π<sub>0</sub> method = "smoother", π<sub>0</sub> will be estimated by applying a smoother to a scatterplot of log(π<sub>0</sub>) estimates against the tuning parameter λ. Optional.
transformation method Either a "probit" or "logit" transformation is applied to the p-values so that a local FDR estimate can be formed that does not involve edge effects of the [0,1] interval in which the p-values lie.
truncate local FDR values If TRUE, local FDR values >1 are set to 1. Default is TRUE.
monotone If TRUE, local FDR values are non-decreasing with increasing p-values. Default is TRUE; this is recommended.
adjust Numeric value that is applied as a multiple of the smoothing bandwidth used in the density estimation. Default is adj=1.5. This value is directly assigned to the adjust argument of the density function.
threshold Numeric value that is threshold for the tails of the empirical p-value distribution. Default is 10<sup>-8</sup>.
FDR level A level at which to control the FDR. Must be in (0,1]. Optional; if this is selected, a vector of TRUE and FALSE is returned that specifies whether each q-value is less than fdr level or not.
pfdr An indicator of whether it is desired to make the estimate more robust for small p-values and a direct finite sample estimate of pFDR -- optional.