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
)
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
orless
) ortwo.sided
test - tip_switch
- maximum tip/switch ratio
- exclude
- exclude clones with tip/switch ratio >
tip_switch
?
Value¶
A list containing a tibble
with mean SP statistics, and another
with SP statistics per repetition.
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 < 0PGT
: p value that DELTA > 0STAT
: Statistic used (SP).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")
# testSP(btrees$switches)
See also¶
Uses output from findSwitches. Related to testPS and testSC.