fisher.method {metaseqR} | R Documentation

## Perform Fisher's Method for combining p-values

### Description

Function for combining p-values by performing Fisher's method. The approach as described by Fisher's combines p-values to a statistic

S = -2 ∑^k \log p

, which follows a χ^2 distribution with 2k degrees of freedom.

### Usage

    fisher.method(pvals, method = c("fisher"), p.corr = c("bonferroni",
    "BH", "none"), zero.sub = 1e-05, na.rm = FALSE, mc.cores=NULL)

### Arguments

`pvals` | A matrix or data.frame containing the p-values from the single tests
`method` | A string indicating how to combine the p-values for deriving a sumary p-value. Currently only the classical approach described by Fisher is implemented.
`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
`na.rm` | A flag indicating whether NA values should be removed from the analysis.
`mc.cores` | Currently ignored

### Details

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This function was copied from the CRAN package MADAM which is no longer maintained.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

Fisher, R.A. (1925). Statistical Methods for Research Workers. Oliver and Boyd (Edinburgh). Moreau, Y.et al. (2003). Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends in Genetics, 19(10), 570-577.

### See Also

`fisher.method.perm`

### Examples

    set.seed(123)
    pp <- matrix(c(runif(20),c(0.001,0.02,0.03,0.001)), ncol=4)
    pp[2,3] <- NA
    fisher.method(pp) #returns one NA row
    fisher.method(pp, na.rm=TRUE) #ignore NA entry in that row

[Package metaseqR version 1.28.0 Index]