Description Usage Arguments Details Value See Also Examples
Performs one-sample and two-sample Fluctuation Analysis tests on mutant counts. Returns confidence intervals and p-values, based on asymptotic normality, from the values returned by mutestim
.
1 2 3 4 5 6 7 | flan.test(mc,fn=NULL,mfn=NULL,cvfn=NULL, # user's data
fitness=NULL,death=0, # user's parameters
mutations0=1,mutprob0=NULL,fitness0=1, # null hypotheses
conf.level=0.95, # confidence level
alternative=c("two.sided","less","greater"), # alternative
method=c("ML","GF","P0"),winsor=512, # estimation method
model=c("LD","H")) # clone growth model
|
mc |
a numeric vector of mutant counts or a list of two numeric vectors of mutant counts. |
fn |
an optional numeric vector of final numbers or a list of two numeric vectors of final numbers. |
mfn |
mean final number of cells. Ignored if |
cvfn |
coefficient of variation of final number of cells. Ignored if |
fitness |
fitness parameter: ratio of growth rates of normal and mutant cells. If |
death |
death probability. Must be smaller than 0.5. |
mutations0 |
null hypothesis value for parameter mutations. See details. |
mutprob0 |
null hypothesis value for parameter mutprob. See details. |
fitness0 |
null hypothesis value for parameter fitness. See details. |
alternative |
a character string specifying the alternative hypothesis, must be one of |
conf.level |
confidence level of the interval. |
method |
estimation method as a character string: one of |
winsor |
winsorization parameter: positive integer. Only used when |
model |
statistical lifetime model as a character string: one of |
flan.test
tests the values of parameters mutations
, mutprob
, or fitness
, with mutations0
mutprob0
, fitness0
as null hypotheses. If fn
or mfn
are given, mutprob is tested, otherwise, mutations
is tested. If fitness
is given, it is not tested.
alternative
may be a two dimensional vector specifying the alternatives for the two parameters to be tested.
For the two-sample tests, the values in mutations0
, mutprob0
and fitness0
apply to the difference between the two samples.
Returns a list with class "flantest"
. The structure of a "flantest"
object, is similar to that of a "htest"
object (see also t.test
).
The class "flantest"
contains the following components :
Tstat |
the value of the computed statistic(s). |
parameter |
the values of |
p.value |
the p-value(s) of the test. |
conf.int |
confidence interval(s) for the parameter(s) relative to the specified alternative. |
estimates |
the estimate(s). |
null.value |
the specified hypothesized value(s). |
alternative |
a (vector of) character string(s) describing the alternative hypothesis. |
model |
the statistical lifetime model. |
method |
method used to compute the estimate(s). |
data.name |
a character string giving the name of the complete data. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | # one sample test, without final numbers
b <- unlist(boeal)
# is the mean mutation number greater than 0.7, and the fitness greater than 0.8?
flan.test(b,alternative="greater",mutations0=0.7,fitness0=0.8)
# is the mean mutation number less than 0.8, given the fitness?
flan.test(b,alternative="less",mutations0=0.8,fitness=0.84)
# one sample test, with final numbers
d <- david[[11]]
flan.test(d$mc,d$fn,alternative="less",mutprob0=2e-10,fitness0=2)
# two-sample test: test equality of parameters
b1 <- unlist(boeal[1:10])
b2 <- unlist(boeal[11:20])
flan.test(list(b1,b2))
# realistic random sample of size 100: mutation probability 1e-9,
# mean final number 1e9, coefficient of variation on final numbers 0.3,
# fitness 0.9, lognormal lifetimes, 5% mutant deaths
x <- rflan(100,mutprob=1e-9,mfn=1e9,cvfn=0.3,fitness=0.9,death=0.05)
# test on mutations and fitness, without final numbers
flan.test(x$mc,mutations0=1,fitness0=0.9)
# test on mutprob and fitness, with final numbers
flan.test(x$mc,x$fn,mutprob0=1e-9,fitness0=0.9)
# given fitness
flan.test(x$mc,x$fn,fitness=0.9,mutprob0=1e-9)
# take deaths into account
flan.test(x$mc,x$fn,mutprob0=1e-9,fitness0=0.9,death=0.05)
# change method
flan.test(x$mc,x$fn,mutprob0=1e-9,fitness0=0.9,death=0.05,method="GF")
flan.test(x$mc,x$fn,mutprob0=1e-9,fitness0=0.9,death=0.05,method="P0")
# change model
flan.test(x$mc,x$fn,mutprob0=1e-9,fitness0=0.9,model="H")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.