boeal: Number of nalidixic acid-resistant mutants from Boe et al....

In flan: FLuctuation ANalysis on Mutation Models

Description

Samples from Table 4 p. 2784-2785 of Boe and al (1994).

Plates with more than 512 mutants could not be counted with precision, hence the value 512 must be understood as “512 or more”.

Usage

  data(boeal)

Format

A list of 23 samples of mutants counts, each named "B<index of the sample>".

The i-th sample of the list includes the i-th column of the table.

Source

L. Boe, T. Tolker-Nielsen, K. M. Eegholm, H. Spliid, and A. Vrang: Fluctuation analysis of mutations to nalidixic acid resistance in Escherichia Coli, J. Bacteriol., 176(10):2781-2787 (1994)

Examples

b <- unlist(boeal)              # concatenate all samples
ml <- mutestim(b)               # maximum likelihood
gf <- mutestim(b,method="GF")   # generating function
p0 <- mutestim(b,method="P0")   # P0 method
cbind(ml,gf,p0)                 # compare 3 methods

                                # test values of mutations and fitness
flan.test(b,alternative=c("greater","less"),mutations0=0.6,fitness0=1)

b1 <- unlist(boeal[1:10])       # first 10 samples
b2 <- unlist(boeal[11:20])      # next 10 samples
flan.test(list(b1,b2))          # test equality

Example output

             ml         gf         p0        
mutations    0.7139283  0.7109608  0.7095859 
sd.mutations 0.02982235 0.02990844 0.03059123
fitness      0.8379082  0.8208731  0.8367936 
sd.fitness   0.0412546  0.04353685 0.04042961

	One sample ML-test (LD model)

--------------------------------- Data -------------------------------
data:  b
Sample parameters: death = 0, plateff = 1
------------------------------ Statistics ----------------------------
Tstat = (3.8202 , -3.9291)
p-value for mutation number  =  6.666e-05 
p-value for fitness  =  4.264e-05 
Alternative hypotheses: true mutation number is greater than 0.6
                        true fitness is less than 1
95 percent confidence interval for mutation number: 
0.6648749         Inf
95 percent confidence interval for fitness: 
0.000000   0.905766
Sample estimates: 
mutation number         fitness 
      0.7139283       0.8379082 


	Two sample ML-test (LD model)

--------------------------------- Data -------------------------------
data:  list(b1, b2)1 and list(b1, b2)2
Sample 1 parameters: death = 0, plateff = 1
Sample 2 parameters: death = 0, plateff = 1
------------------------------ Statistics ----------------------------
Tstat = (0.39237 , -0.106)
p-value for mutations difference  =  0.6948 
p-value for fitness difference  =  0.9156 
Alternative hypotheses: true mutations difference is not equal to 0
                        true fitness difference is not equal to 0
95 percent confidence interval for mutations difference: 
-0.09925847    0.14894662
95 percent confidence interval for fitness difference: 
-0.1760990    0.1580278
Sample 1 estimates: 
mutation number         fitness 
      0.7149185       0.7993262 
Sample 2 estimates: 
mutation number         fitness 
      0.6900744       0.8083618 

flan documentation built on June 7, 2021, 9:07 a.m.