testPS: Performs PS (parsimony score) test on switch data

In dowser: B Cell Receptor Phylogenetics Toolkit

Performs PS (parsimony score) test on switch data

Description

testPS performs a PS test

Usage

testPS(
  switches,
  bylineage = FALSE,
  pseudocount = 0,
  alternative = c("less", "two.sided", "greater")
)

Arguments

switches	Data frame from findSwitches
bylineage	Perform test for each lineage individually? (FALSE)
pseudocount	Pseudocount for P value calculations
alternative	Perform one-sided (greater or less) or two.sided test

Details

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

• RECON: PS for observed data.

• PERMUTE: PS for permuted data.

• DELTA: RECON - PERMUTE.

• PLT: p value that DELTA < 0

• PGT: p value that DELTA > 0

• STAT: Statistic used (PS).

• REP: Bootstrap repetition.

• REPS: Total number of ootstrap repetition.

Value

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

See Also

Uses output from findSwitches. Related to testSP and testSC.

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=10, nproc=1,
   igphyml=igphyml, trait="sample_id")
testPS(btrees$switches)

## End(Not run)

dowser documentation built on May 29, 2024, 3:06 a.m.