Analysis.permutation: Computing the FDR-controlled level for the significance of...
In R2GUESS: Wrapper Functions for GUESS

Description Usage Arguments Value Author(s) See Also Examples

Reads outputs from a preliminary set of permutation runs of GUESS mimicking the null hypothesis of no association (shuffling the responses). Results will subsequently be used to derive the cut-off values for the Marginal Posterior Probability Inclusion of (MPPI ) ensuring an empirical FDR control at a user-defined level. Several cut-off values will be investigated and, for each, the corresponding empirical FDR will be returned. The cut-off value providing the closest FDR estimate to the desired level will be retained. Exact match to the desired level will be achieved by linear interpolation. For flexibility, Analysis.permutation only performs the calculation of the FDR-controlled cut-off value based on a preliminary set of permuted runs of GUESS, while the function FDR.permutation - which is based on the same procedure - also includes the permutations.

1 2	Analysis.permutation(x, Npermut, namePermut, threshold = 0.05, path.output, number.cutoff=200)

`x`	an object of class "ESS".
`Npermut`	number of permutation runs to base the FDR calculations on. If the number exceeds the number of actual permutations then the calculation will stop and the function will return an error.
`namePermut`	name specifying the file name stem locating where results from the preliminary permutation runs were stored.
`threshold`	numeric value specifying the desired the FDR level.
`path.output`	path directory containing the output files of the permuted runs.
`number.cutoff`	numeric value specifying the number of points on which to be base the FDR estimation.

Analysis.permutation returns a list containing the following fields:

`cutoff.MPI`	The MPPI threshold to control empirical FDR at a specified level.
`cutoff_int`	The linearly interpolation (across the `number.cutoff` points) cut-off value of MPPI exactly controlling the FDR at the specified level.
`cutoff_St`	the vector of cutoff values investigated (containing `number.cutoff` elements).
`FDR_emp`	Empirical FDR corresponding to the `cutoff.MPI` value.
`FDR_emp_int`	Empirical FDR value estimated by linear interpolation for the `cutoff_int` value.
`FDR_emp_St`	A vector of empirical FDR values computed by linear interpolation for each `cutoff_St` values investigated.

Benoit Liquet, b.liquet@uq.edu.au,
Marc Chadeau-Hyam m.chadeau@imperial.ac.uk,
Leonardo Bottolo l.bottolo@imperial.ac.uk,
Gianluca Campanella g.campanella11@imperial.ac.uk

FDR.permutation

## Not run: 
path.output.perm <- tempdir()
path.input.perm <-path.output.perm

cutoff.1 <- FDR.permutation(x=modelY_Hopx,Npermut=6,start.counter=1,
          path.output=path.output.perm,path.input=path.input.perm,nbcpu=3)

cutoff.2 <- FDR.permutation(x=modelY_Hopx,Npermut=6,start.counter=7,
          path.output=path.output.perm,path.input=path.input.perm,nbcpu=3)

namePermut <- "Permut-Example-GUESS-Y-Hopx"

cutoff.pool <-Analysis.permutation(modelY_Hopx,namePermut=namePermut,
      Npermut=9,threshold=0.05,path.output=path.output.perm,number.cutoff=10)

## End(Not run)