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

Description

testSC performs an SC test

Usage

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

Value

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

Arguments

switches: Data frame from findSwitches
dropzeroes: 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

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

Run this code

if (FALSE) {
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)
}