runCorrelationTest {dowser}

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?

Details

See correlationTest for details

Value

A list of statistics from running the permutation test.

See Also

correlationTest.