testPS

testPS - 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

Value¶

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

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 bootstrap repetition.

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)