testSC - Performs SC (switch count) test on switch data

Description

testSC performs an SC test

Usage

testSC(
switches,
dropzeros = TRUE,
bylineage = FALSE,
pseudocount = 0,
from = NULL,
to = NULL,
permuteAll = FALSE,
alternative = c("two.sided", "greater", "less")
)

Arguments

switches
Data frame from findSwitches
dropzeros
Drop switches with zero counts?
bylineage
Perform test for each lineage individually?
pseudocount
Pseudocount for P value calculations
from
Include only switches from this state?
to
Include only switches to this state?
permuteAll
Permute among trees?
alternative
Perform one-sided (greater or less) or two.sided test

Value

A list containing a tibble with mean SC statistics, and another with SC statistics per repetition.

Details

Output data table columns: RECON = SC for observed data PERMUTE = SC for permuted data DELTA = RECON - PERMUTE PLT = p value for DELTA < 0 PGT = p value for DELTA < 0

  • FROM: State going from.
  • TO: State going to.
  • RECON: SC for observed data.
  • PERMUTE: SC for permuted data.
  • DELTA: RECON - PERMUTE.
  • PLT: p value that DELTA < 0
  • PGT: p value that DELTA > 0
  • STAT: Statistic used (SC).
  • REP: Bootstrap repetition.
  • REPS: Total number of ootstrap repetition.

Examples

### Not run:
igphyml <- "~/apps/igphyml/src/igphyml"
# data(ExampleAirr)
# ExampleAirr$sample_id = sample(ExampleAirr$sample_id)
# clones = formatClones(ExampleAirr, trait="sample_id")
# btrees = findSwitches(clones[1:2], bootstraps=100, nproc=1,
# igphyml=igphyml, trait="sample_id", id="temp", dir="temp")
# testSC(btrees$switches)

See also

Uses output from findSwitches. Related to testPS and testSP.