truncated {metap}

Truncated product methods

Description

Implements two procedures for truncated versions of Fisher's method

Usage

truncated(p, ptrunc = NULL, rtrunc = NULL, ...)
## S3 method for class 'truncated'
print(x, ...)
## S3 method for class 'truncated'
summary(object, ...)
## S3 method for class 'truncated'
plot(x, pparams = list(pchs = c(16, 1),
   pcols = c("black", "black")), ...)

Arguments

p

A vector of significance values

ptrunc

Value of \(p\) to truncate at. See Details

rtrunc

Which rank \(p\) to truncate at. See Details

x

An object of class ‘truncated’

object

An object of class ‘truncated’

...

Other arguments to be passed through

pparams

A list containing a vector pchs of plotting symbols and a vector pcols of colours

Details

Uses routines from TFisher to implement truncated Fisher (Zaykin et al. 2007; Zhang et al. 2018) and from mutoss to implement rank-truncated Fisher (Dudbridge and Koeleman 2003)

The print method prints the statistic and its associated \(p\)-value. The summary method also prints how many of the input values were actually used. The plot method provides an index plot of the \(p\)-values. By default used \(p\)-values are plotted with a black filled circle and those not used with a black unfilled circle. The colours and plotting symbols can be changed in pparams. The first element of each vector is for the used \(p\)-values and the second for the unused ones.

Value

An object of class ‘truncated’ a list with entries

p

The resultant overall \(p\)-value

stat

The test statistic

validp

The input vector with illegal values removed

ptrunc

The \(p\)-value used for truncation

trunc

The rank value used for truncation

n

A vector containing incl, the number of valid values included, excl, the number of valid values not used

method

The method used

Note

Only one of ptrunc or rtrunc is returned as appropriate. If the function encounters an error it returns NA for the value of p and gives a warning message. The effect of specifying both ptrunc and rtrunc is undefined.

Author(s)

Michael Dewey

References

Dudbridge F, Koeleman BPC (2003). “Rank truncated product of P–values, with application to genomewide association scans.” Genetic Epidemiology, 25, 360–366.

Zaykin DV, Zhivotovsky LA, Czika W, Shao S, Wolfinger RD (2007). “Combining p–values in large–scale genomics experiments.” Pharmaceutical Statistics, 6, 217–236.

Zhang H, Tong T, Landers J, Wu Z (2018). “TFisher tests: optimal and adaptive thresholding for combining p–values.” arXiv. https://arxiv.org/abs/1801.04309.

See Also

ranktruncated, stat.tpm, and p.tpm

Examples

data(dat.metap)
validity <- dat.metap$validity
truncated(validity, ptrunc = 0.5)
truncated(validity, rtrunc = 5)