testSP: Performs SP (switch proportion) test on switch data

In dowser: B Cell Receptor Phylogenetics Toolkit

Performs SP (switch proportion) test on switch data

Description

testSP performs an SP test

Usage

testSP(
  switches,
  permuteAll = FALSE,
  from = NULL,
  to = NULL,
  dropzeroes = TRUE,
  bylineage = FALSE,
  pseudocount = 0,
  alternative = c("greater", "two.sided", "less"),
  tip_switch = 20,
  exclude = FALSE
)

Arguments

switches	Data frame from findSwitches
permuteAll	Permute among trees?
from	Include only switches from this state?
to	Include only switches to this state?
dropzeroes	Drop switches with zero counts?
bylineage	Perform test for each lineage individually?
pseudocount	Pseudocount for P value calculations
alternative	Perform one-sided (greater or less) or two.sided test
tip_switch	maximum tip/switch ratio
exclude	exclude clones with tip/switch ratio > tip_switch?

Details

Output data table columns: RECON = SP for observed data PERMUTE = SP 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: SP for observed data.

• PERMUTE: SP for permuted data.

• DELTA: RECON - PERMUTE.

• PLT: p value that DELTA < 0

• PGT: p value that DELTA > 0

• STAT: Statistic used (SP).

• REP: Bootstrap repetition.

• REPS: Total number of ootstrap repetition.

Value

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

See Also

Uses output from findSwitches. Related to testPS 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")
testSP(btrees$switches)

## End(Not run)

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