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
orless
) ortwo.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 < 0PGT
: p value that DELTA > 0STAT
: Statistic used (PS).REP
: Bootstrap repetition.REPS
: Total number of ootstrap 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)
See also¶
Uses output from findSwitches. Related to testSP and testSC.