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

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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

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.sum, fisher.method.perm

Examples

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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