testSP: 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
)

Value

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

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.

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