runCorrelationTest - Run correlationTest, based on https://doi.org/10.1111/2041-210X.12466
Description¶
runCorrelationTest performs root-to-tip regression permutation test
Usage¶
runCorrelationTest(
phy,
clone,
permutations,
minlength = 0.001,
polyresolve = TRUE,
permutation = c("clustered", "uniform"),
time = "time",
sequence = "sequence_id",
germline = "Germline",
verbose = TRUE,
alternative = c("greater", "two.sided")
)
Arguments¶
- phy
- Tree object
- clone
- airrClone data object corresponding to
phy - permutations
- Number of permutations to run
- minlength
- Branch lengths to collapse in trees
- polyresolve
- Resolve polytomies to have a minimum number of single timepoint clades
- permutation
- Permute among single timepoint clades or uniformly among tips
- time
- Column name holding numeric time information
- sequence
- Column name holding sequence ID
- germline
- Germline sequence name
- verbose
- Print lots of rubbish while running?
- alternative
- Is alternative that the randomized correlation are greater than or equal to observed, or greater/less than?
Value¶
A list of statistics from running the permutation test.
Details¶
See correlationTest for details