testSC - Performs SC (switch count) test on switch data
Description¶
testSC
performs an SC test
Usage¶
testSC(
switches,
dropzeroes = TRUE,
bylineage = FALSE,
pseudocount = 0,
from = NULL,
to = NULL,
permuteAll = FALSE,
alternative = c("two.sided", "greater", "less")
)
Arguments¶
- switches
- Data frame from findSwitches
- dropzeroes
- Drop switches with zero counts?
- bylineage
- Perform test for each lineage individually?
- pseudocount
- Pseudocount for P value calculations
- from
- Include only switches from this state?
- to
- Include only switches to this state?
- permuteAll
- Permute among trees?
- alternative
- Perform one-sided (
greater
orless
) ortwo.sided
test
Value¶
A list containing a tibble
with mean SC statistics, and another
with SC statistics per repetition.
Details¶
Output data table columns: RECON = SC for observed data PERMUTE = SC 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
: SC for observed data.PERMUTE
: SC for permuted data.DELTA
: RECON - PERMUTE.PLT
: p value that DELTA < 0PGT
: p value that DELTA > 0STAT
: Statistic used (SC).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=100, nproc=1,
# igphyml=igphyml, trait="sample_id", id="temp", dir="temp")
# testSC(btrees$switches)
See also¶
Uses output from findSwitches. Related to testPS and testSP.