testSC {dowser}

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")
)

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.

Value

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

See Also

Uses output from findSwitches. Related to testPS and testSP.

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)

## End(Not run)