combineParallelPValues: Combine parallel p-values

In LTLA/metapod: Meta-Analyses on P-Values of Differential Analyses

Combine parallel p-values

Description

Combine p-values from parallel hypothesis tests using a variety of meta-analysis methods. Each group of p-values is defined from the corresponding entries across all vectors. The function processes all vectors “in parallel” - hence the name.

Usage

combineParallelPValues(
  p.values,
  method = c("simes", "holm-min", "berger", "fisher", "pearson", "wilkinson",
    "stouffer"),
  weights = NULL,
  log.p = FALSE,
  min.n = 1,
  min.prop = 0.5
)

Arguments

p.values	A list of numeric vectors of the same length, containing the p-values to be combined.
method	String specifying the method to use to combine p-values.
weights	A numeric vector of positive weights, with one value per vector in .... Each weight is applied to all entries of itscorresponding vector, i.e., all p-values in that vector receive the same weight. Alternatively, a list of numeric vectors of weights with the same structure as p.values. Each p-value is then assigned the weight in the corresponding entry of weights. Alternatively NULL, in which case all p-values are assigned equal weight.
log.p	Logical scalar indicating whether the p-values in p.values are log-transformed.
min.n	Integer scalar specifying the minimum number of individual nulls to reject when testing the joint null.
min.prop	Numeric scalar in [0, 1], specifying the minimum proportion of individual nulls to reject when testing the joint null.

Details

min.prop and min.n only have an effect for method="wilkinson" and "holm-min".

weights only has an effect for method="simes", "holm-min" and "stouffer".

Value

A list containing:

• p.value, a numeric vector of length equal to the length of each vector in p.values. This contains the Simes p-value for each group, log-transformed if log.p=TRUE.

• representative, an integer scalar specifying the representative test in each group. Specifically, this refers to the index of the vector of p.values containing the representative test.

• influential, a list of logical vectors mirroring the structure of p.values. Entries are TRUE for any p-value that is deemed “influential” to the final combined p-value.

Author(s)

Aaron Lun

Examples

p1 <- runif(10000)
p2 <- runif(10000)
p3 <- runif(10000)

fish <- combineParallelPValues(list(p1, p2, p3), method="fisher")
hist(fish$p.value)

z <- combineParallelPValues(list(p1, p2, p3), method="stouffer", weights=1:3)
hist(z$p.value)

simes <- combineParallelPValues(list(p1, p2, p3), method="simes")
hist(simes$p.value)

berger <- combineParallelPValues(list(p1, p2, p3), method="berger")
hist(berger$p.value)

LTLA/metapod documentation built on Jan. 19, 2024, 11:49 p.m.