Description Usage Arguments Value Author(s) See Also Examples
View source: R/Analysis.permutation.R
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
|
cutoff_St |
the vector of cutoff values investigated (containing
|
FDR_emp |
Empirical FDR corresponding to the |
FDR_emp_int |
Empirical FDR value estimated by linear interpolation for the |
FDR_emp_St |
A vector of empirical FDR values computed by
linear interpolation for each |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
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