View source: R/combineGroupedPValues.R
combineGroupedPValues | R Documentation |
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.
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
)
p.values |
A numeric vector containing p-values for individual tests. |
grouping |
A vector or factor of length equal to Alternatively, an rle object where each run corresponds to a group and specifies the entries of |
method |
String specifying the method to use to combine p-values. |
weights |
A numeric vector of length equal to |
log.p |
Logical scalar indicating whether the p-values in |
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. |
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"
.
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.
Aaron Lun
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.