combineGroupedPValues: Combine grouped p-values

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

Combine grouped p-values

Description

Combine p-values from grouped hypothesis tests using a variety of meta-analysis methods. Each group of p-values is defined as those assigned to the same level of the grouping factor.

Usage

combineGroupedPValues(
  p.values,
  grouping,
  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 numeric vector containing p-values for individual tests.
grouping	A vector or factor of length equal to p.values, specifying the group to which each test is assigned. Alternatively, an rle object where each run corresponds to a group and specifies the entries of p.values belonging to that group. This assumes that p.values is ordered such that all entries in the same group are adjacent to each other.
method	String specifying the method to use to combine p-values.
weights	A numeric vector of length equal to p.values, containing a positive weight for each test. Alternatively NULL, in which case equal weights are assigned to all tests.
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 named numeric vector of length equal to the number of unique levels in grouping. This contains the combined p-value for each group, log-transformed if log.p=TRUE. Each entry is named according to the group.

• representative, a named integer scalar specifying the index of representative test for each group. Each index refers to an entry of p.values and is named according to its group.

• influential, a logical vector of length equal to p.values. Entries are TRUE for any p-value that is deemed “influential” to the final combined p-value for its group.

Author(s)

Aaron Lun

Examples

p <- runif(10000)
g <- sample(100, 10000, replace=TRUE)

fish <- combineGroupedPValues(p, g, method="fisher")
hist(fish$p.value)

z <- combineGroupedPValues(p, g, method="stouffer", weights=rexp(10000))
hist(z$p.value)

simes <- combineGroupedPValues(p, g, method="simes")
hist(simes$p.value)

berger <- combineGroupedPValues(p, g, method="berger")
hist(berger$p.value)

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