fisher.method: Perform Fisher's Method for combining p-values

In MADAM: This package provides some basic methods for meta-analysis

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

Author(s)

Karl Kugler <[e-mail]>

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

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

Example output

          S num.p     p.value       p.adj
1  6.777894     4 0.560775005 0.560775005
2        NA     4          NA          NA
3 21.341682     4 0.006293087 0.015732716
4  9.851807     4 0.275581603 0.344477004
5 10.028259     4 0.263048102 0.344477004
6 27.912704     4 0.000491135 0.002455675
           S num.p     p.value      p.adj
1  6.7778939     4 0.560775005 0.67293001
2  0.7965067     3 0.992167008 0.99216701
3 21.3416818     4 0.006293087 0.01887926
4  9.8518073     4 0.275581603 0.41337240
5 10.0282590     4 0.263048102 0.41337240
6 27.9127045     4 0.000491135 0.00294681

MADAM documentation built on May 2, 2019, 5:18 p.m.