cosinePerm {CoreGx} | R Documentation |
Cosine Permutations
Description
Computes the cosine similarity and significance using permutation test. This
function uses random numbers, to ensure reproducibility please call
set.seed()
before running the function.
Usage
cosinePerm(
x,
y,
nperm = 1000,
alternative = c("two.sided", "less", "greater"),
include.perm = FALSE,
nthread = 1,
...
)
Arguments
x |
factor is the factors for the first variable
|
y |
factor is the factors for the second variable
|
nperm |
integer is the number of permutations to compute the null
distribution of MCC estimates
|
alternative |
string indicates the alternative hypothesis and
must be one of ‘'two.sided'’, ‘'greater'’ or ‘'less'’. You can specify
just the initial letter. ‘'greater'’ corresponds to positive association,
‘'less'’ to negative association. Options are 'two.sided', 'less', or
'greater'
|
include.perm |
boolean indicates whether the estimates for the
null distribution should be returned. Default set to 'FALSE'
|
nthread |
integer is the number of threads to be used to perform
the permutations in parallel
|
... |
A list of fallthrough parameters
|
Value
A list
estimate of the cosine similarity, p-value and
estimates after random permutations (null distribution) in include.perm is
set to 'TRUE'
Examples
x <- factor(c(1,2,1,2,1))
y <- factor(c(2,2,1,1,1))
cosinePerm(x, y)
[Package
CoreGx version 1.6.0
Index]