fisher.method.perm {metaseqR} | R Documentation

## Derive a p-value for a summary statistic of p-values by permutation

### Description

Given a set of p-values and a summary statistic S:

S = -2 ∑ \log p,

a p-value for this statistic can be derived by randomly generating summary statistics [Rhodes,2002]. Therefore, a p-value is randomly sampled from each contributing study and a random statistic is calculated. The fraction of random statistics greater or equal to S then gives the p-value.

### Usage

      fisher.method.perm(pvals, p.corr = c("bonferroni", "BH", "none"),
      zero.sub = 1e-05, B = 10000, mc.cores = NULL, blinker = 1000)

### Arguments

`pvals` | A matrix or data.frame containing the p-values from the single tests
`p.corr` | Method for correcting the summary p-values. BH: Benjamini-Hochberg (default); Bonferroni's method or no ('none') correction are currently supported.
`zero.sub` | Replacement for p-values of 0
`B` | Number of random statistics
`mc.cores` | Number of cores used for calculating the permutations. If not `NULL` the `multicore` package is used for parallelization with the given number of cores.
`blinker` | An indicator that prints "`=`" after each `blinker` rows of `pvals` in order to follow the progress.

### Details

At the moment this function only supports situations were all passed p-values are not `NA`. We plan on extending this functionality in upcoming versions.

For large data sets and/or large `B` we strongly recommend using the `mc.cores` option as the calculation will otherwise be computationally demanding. This will call the `mclapply` function from the multicore package, which you will have to install in that case.

By default a blinker (a small string "=") is shown after each 1000 rows that were computed. This function allows you to assess the progress of the analysis. If you don't want to see the blinker set it to `NA`.

As `log(0)` results in `Inf` we replace p-values of 0 by default with a small float. If you want to keep them as 0 you have to provide 0 as a parameter in `zero.sub`.

Note that only p-values between 0 and 1 are allowed to be passed to this method.

### Value

This method returns a data.frame containing the following columns

`S` | The statistic
`num.p` | The number of p-values used to calculate S
`p.value` | The overall p-value
`p.adj` | The adjusted p-value

### Note

This function was copied from the CRAN package MADAM which is no longer maintained. Recognition goes to the original author(s) below.

### Author(s)

Karl Kugler <karl@eigenlab.net>

### References

Rhodes, D. R., (2002). Meta-analysis of microarrays: interstudy alidation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer research, 62(15), 4427-33.

### See Also

`fisher.sum`, `fisher.method`

### Examples

      set.seed(123)
      pp <- matrix(c(runif(20),c(0.001,0.02,0.03,0.001)), ncol=4)
      fisher.method.perm(pp, B=10, blinker=1)
      ## Not run:
        fisher.method.perm(pp, B=10000, mc.cores=3, blinker=1) #use multicore

    ## End(Not run)

[Package metaseqR version 1.28.0 Index]