cellsurvLQfit: Fit the linear-quadratic (LQ) model to cell survival data
In CFAssay: Statistical analysis for the Colony Formation Assay
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
View source: R/cellsurvLQfit.R
Description
This function calculates the linear coefficient alpha and the coefficient beta of the dose-squared term (see manual for this R-package) for colony counts measured for a set of irradiation doses and repeated experiments. The function is a wrapper for the R-functions glm or lm, which simplifies use of these functions for cell survival data.
Usage
1
cellsurvLQfit(X, method="ml", PEmethod="fit")
Arguments
X
A data frame which contains at least columns Exp, dose, ncells, ncolonies and if there is no 0-value in the dose-column, X has to contain a further column pe for plating efficiencies.
method
Determines the method used for the fit. "ml" is for maximum-likelihood, "ls" for least-squares. "franken" performs weigthed least-squares with weights as described in Franken et al. (2006).
PEmethod
Controls the value of the plating efficiencies, i.e. the colony counts for untreated cells. "fit" calculates fitted plating efficiencies as model parameters, "fix" uses fixed ones calculated from the observed zero dose data or from a column named pe in X.
Details
In the data frame X, Exp identifies the experimental replicates and may be numeric or non-numeric. method="ml" uses R function glm with quasipoisson family and link function "log". method="ls" uses R function lm. PEmethod="fit" fits plating efficiencies for every experiments. PEmethod="fix" uses observed plating efficiencies. If there is no 0-value in the dose-column, PEmethod is overwritten with "fix" and X has to contain a further column pe containing the plating efficiencies, i.e. ncolonies/ncells from untreated cells, not per hundred or percent.
Value
The function returns an object of class cellsurvLQfit, which is similar to classes glm or lm, however containing two additional entries, type and PEmethod, which are used for printing and plotting. The full result is returned invisibly, i.e. the function has to be used with print or plot or assigned to a variable, say for e.g. fit as in the example below.
Author(s)
Herbert Braselmann
References
Franken NAP, Rodermond HM, Stap J, et al. Clonogenic assay of cells in vitro. Nature Protoc 2006;1:2315-19.
See Also
glm and family with references for generalized linear modelling, lm
Examples
1
2
3
4
5
6
7
8
9
10
11
datatab<- read.table(system.file("doc", "expl1_cellsurvcurves.txt", package="CFAssay"), header=TRUE, sep="\t")
X<- subset(datatab, cline=="okf6TERT1")
fit<- cellsurvLQfit(X) #using default options
print(fit)
print(fit$type)
print(fit$PEmethod)
#Using other options:
print(cellsurvLQfit(X, method="ls"))
print(cellsurvLQfit(X, PEmethod="fix"))
print(cellsurvLQfit(X, method="ls", PEmethod="fix"))
print(cellsurvLQfit(X, method="franken"))
Example output
method = ml
PEmethod = fit
dose dose2
-0.51937898 -0.02102614
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ml
PEmethod = fit
Logarithmic plating efficiencies PE fitted as intercepts
see remark in the manual, 1.2
Estimate Std. Error t value Pr(>|t|)
PEe1 -1.606686 0.1061229 -15.13986 1.112338e-17
PEe2 -1.693346 0.1090082 -15.53412 4.781145e-18
PEe3 -2.010377 0.1228551 -16.36380 8.506670e-19
PEe4 -1.869228 0.1165115 -16.04329 1.644185e-18
PEe5 -2.052405 0.1069872 -19.18365 3.828727e-21
PEe6 -2.219654 0.1333357 -16.64711 4.789596e-19
PEe7 -2.434634 0.1455642 -16.72550 4.091214e-19
PEe8 -2.109080 0.1258530 -16.75828 3.830883e-19
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.51937898 0.05889260 -8.819088 9.943331e-11
beta -0.02102614 0.00978985 -2.147749 3.817362e-02
Observed and fitted plating efficiencies (%):
Experiment PE PEfitted
PEe1 e1 19.0 20.1
PEe2 e2 17.3 18.4
PEe3 e3 10.0 13.4
PEe4 e4 15.0 15.4
PEe5 e5 9.2 12.8
PEe6 e6 17.0 10.9
PEe7 e7 14.3 8.8
PEe8 e8 11.5 12.1
Residual Deviance: 167.8964
Total residual sum of weighted squares rsswTot: 164.8109
Residual Degrees of Freedom: 38
Dispersion parameter: 4.337128
Fraction rssw of rsswTot per Experiment
Experiment rssw perCent
1 e1 4.84 2.9
2 e2 14.91 9.0
3 e3 9.01 5.5
4 e4 4.51 2.7
5 e5 34.77 21.1
6 e6 52.22 31.7
7 e7 41.09 24.9
8 e8 3.46 2.1
[1] "cfa" "ml"
[1] "fit"
method = ls
PEmethod = fit
dose dose2
-0.53514763 -0.02274424
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ls
PEmethod = fit
Logarithmic plating efficiencies PE fitted as intercepts
see remark in the manual, 1.2
Estimate Std. Error t value Pr(>|t|)
PEe1 -1.547331 0.1462255 -10.58181 6.927387e-13
PEe2 -1.638576 0.1462255 -11.20581 1.314850e-13
PEe3 -1.938002 0.1462255 -13.25351 7.956357e-16
PEe4 -1.809225 0.1462255 -12.37284 6.716913e-15
PEe5 -1.966738 0.1462255 -13.45003 5.005332e-16
PEe6 -2.342463 0.1462255 -16.01953 1.727191e-18
PEe7 -2.516963 0.1462255 -17.21289 1.554955e-19
PEe8 -2.055641 0.1462255 -14.05802 1.227136e-16
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.53514763 0.07216231 -7.415888 6.778935e-09
beta -0.02274424 0.01146734 -1.983392 5.458403e-02
Observed and fitted plating efficiencies (%):
Experiment PE PEfitted
PEe1 e1 19.0 21.3
PEe2 e2 17.3 19.4
PEe3 e3 10.0 14.4
PEe4 e4 15.0 16.4
PEe5 e5 9.2 14.0
PEe6 e6 17.0 9.6
PEe7 e7 14.3 8.1
PEe8 e8 11.5 12.8
Total residual sum of squares rssTot: 3.357983
Residual Degrees of Freedom: 38
Multiple R-squared: 0.9954213
Fraction rss of rssTot per Experiment
Experiment rss perCent
1 e1 0.07 2.2
2 e2 0.26 7.8
3 e3 0.24 7.2
4 e4 0.11 3.2
5 e5 0.57 16.9
6 e6 1.25 37.2
7 e7 0.83 24.6
8 e8 0.03 1.0
method = ml
PEmethod = fix
dose dose2
-0.51079080 -0.02274661
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ml
PEmethod = fix
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.51079080 0.05783126 -8.832435 9.562192e-11
beta -0.02274661 0.01186134 -1.917710 6.268676e-02
Residual Deviance: 399.1192
Total residual sum of weighted squares rsswTot: 369.7449
Residual Degrees of Freedom: 38
Dispersion parameter: 9.730129
Fraction rssw of rsswTot per Experiment
Experiment rssw perCent
1 e1 6.39 1.7
2 e2 17.65 4.8
3 e3 43.57 11.8
4 e4 5.15 1.4
5 e5 109.36 29.6
6 e6 96.56 26.1
7 e7 86.86 23.5
8 e8 4.20 1.1
method = ls
PEmethod = fix
dose dose2
-0.53063032 -0.02331461
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ls
PEmethod = fix
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.53063032 0.07510284 -7.065383 2.006471e-08
beta -0.02331461 0.01502057 -1.552179 1.289092e-01
Total residual sum of squares rssTot: 9.398594
Residual Degrees of Freedom: 38
Multiple R-squared: 0.9866913
Fraction rss of rssTot per Experiment
Experiment rss perCent
1 e1 0.14 1.5
2 e2 0.33 3.5
3 e3 1.01 10.7
4 e4 0.15 1.6
5 e5 1.57 16.7
6 e6 3.25 34.6
7 e7 2.85 30.4
8 e8 0.09 1.0
method = franken
PEmethod = fix
dose dose2
-0.4887937 -0.0219078
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = franken
PEmethod = fix
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.4887937 0.05385806 -9.075591 4.709574e-11
beta -0.0219078 0.01106990 -1.979043 5.509104e-02
Total residual sum of weighted squares rsswTot: 335.6884
Residual Degrees of Freedom: 38
Multiple R-squared: 0.9918373
Fraction rssw of rsswTot per Experiment
Experiment rssw perCent
1 e1 5.72 1.7
2 e2 11.98 3.6
3 e3 26.34 7.8
4 e4 5.23 1.6
5 e5 73.15 21.8
6 e6 107.79 32.1
7 e7 99.19 29.5
8 e8 6.28 1.9
CFAssay documentation built on Nov. 8, 2020, 11:10 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/cellsurvLQfit.R
Description
This function calculates the linear coefficient alpha and the coefficient beta of the dose-squared term (see manual for this R-package) for colony counts measured for a set of irradiation doses and repeated experiments. The function is a wrapper for the R-functions glm or lm, which simplifies use of these functions for cell survival data.
Usage
1 | cellsurvLQfit(X, method="ml", PEmethod="fit")
|
Arguments
X |
A data frame which contains at least columns |
method |
Determines the method used for the fit. |
PEmethod |
Controls the value of the plating efficiencies, i.e. the colony counts for untreated cells. |
Details
In the data frame X, Exp identifies the experimental replicates and may be numeric or non-numeric. method="ml" uses R function glm with quasipoisson family and link function "log". method="ls" uses R function lm. PEmethod="fit" fits plating efficiencies for every experiments. PEmethod="fix" uses observed plating efficiencies. If there is no 0-value in the dose-column, PEmethod is overwritten with "fix" and X has to contain a further column pe containing the plating efficiencies, i.e. ncolonies/ncells from untreated cells, not per hundred or percent.
Value
The function returns an object of class cellsurvLQfit, which is similar to classes glm or lm, however containing two additional entries, type and PEmethod, which are used for printing and plotting. The full result is returned invisibly, i.e. the function has to be used with print or plot or assigned to a variable, say for e.g. fit as in the example below.
Author(s)
Herbert Braselmann
References
Franken NAP, Rodermond HM, Stap J, et al. Clonogenic assay of cells in vitro. Nature Protoc 2006;1:2315-19.
See Also
glm and family with references for generalized linear modelling, lm
Examples
1 2 3 4 5 6 7 8 9 10 11 | datatab<- read.table(system.file("doc", "expl1_cellsurvcurves.txt", package="CFAssay"), header=TRUE, sep="\t")
X<- subset(datatab, cline=="okf6TERT1")
fit<- cellsurvLQfit(X) #using default options
print(fit)
print(fit$type)
print(fit$PEmethod)
#Using other options:
print(cellsurvLQfit(X, method="ls"))
print(cellsurvLQfit(X, PEmethod="fix"))
print(cellsurvLQfit(X, method="ls", PEmethod="fix"))
print(cellsurvLQfit(X, method="franken"))
|
Example output
method = ml
PEmethod = fit
dose dose2
-0.51937898 -0.02102614
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ml
PEmethod = fit
Logarithmic plating efficiencies PE fitted as intercepts
see remark in the manual, 1.2
Estimate Std. Error t value Pr(>|t|)
PEe1 -1.606686 0.1061229 -15.13986 1.112338e-17
PEe2 -1.693346 0.1090082 -15.53412 4.781145e-18
PEe3 -2.010377 0.1228551 -16.36380 8.506670e-19
PEe4 -1.869228 0.1165115 -16.04329 1.644185e-18
PEe5 -2.052405 0.1069872 -19.18365 3.828727e-21
PEe6 -2.219654 0.1333357 -16.64711 4.789596e-19
PEe7 -2.434634 0.1455642 -16.72550 4.091214e-19
PEe8 -2.109080 0.1258530 -16.75828 3.830883e-19
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.51937898 0.05889260 -8.819088 9.943331e-11
beta -0.02102614 0.00978985 -2.147749 3.817362e-02
Observed and fitted plating efficiencies (%):
Experiment PE PEfitted
PEe1 e1 19.0 20.1
PEe2 e2 17.3 18.4
PEe3 e3 10.0 13.4
PEe4 e4 15.0 15.4
PEe5 e5 9.2 12.8
PEe6 e6 17.0 10.9
PEe7 e7 14.3 8.8
PEe8 e8 11.5 12.1
Residual Deviance: 167.8964
Total residual sum of weighted squares rsswTot: 164.8109
Residual Degrees of Freedom: 38
Dispersion parameter: 4.337128
Fraction rssw of rsswTot per Experiment
Experiment rssw perCent
1 e1 4.84 2.9
2 e2 14.91 9.0
3 e3 9.01 5.5
4 e4 4.51 2.7
5 e5 34.77 21.1
6 e6 52.22 31.7
7 e7 41.09 24.9
8 e8 3.46 2.1
[1] "cfa" "ml"
[1] "fit"
method = ls
PEmethod = fit
dose dose2
-0.53514763 -0.02274424
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ls
PEmethod = fit
Logarithmic plating efficiencies PE fitted as intercepts
see remark in the manual, 1.2
Estimate Std. Error t value Pr(>|t|)
PEe1 -1.547331 0.1462255 -10.58181 6.927387e-13
PEe2 -1.638576 0.1462255 -11.20581 1.314850e-13
PEe3 -1.938002 0.1462255 -13.25351 7.956357e-16
PEe4 -1.809225 0.1462255 -12.37284 6.716913e-15
PEe5 -1.966738 0.1462255 -13.45003 5.005332e-16
PEe6 -2.342463 0.1462255 -16.01953 1.727191e-18
PEe7 -2.516963 0.1462255 -17.21289 1.554955e-19
PEe8 -2.055641 0.1462255 -14.05802 1.227136e-16
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.53514763 0.07216231 -7.415888 6.778935e-09
beta -0.02274424 0.01146734 -1.983392 5.458403e-02
Observed and fitted plating efficiencies (%):
Experiment PE PEfitted
PEe1 e1 19.0 21.3
PEe2 e2 17.3 19.4
PEe3 e3 10.0 14.4
PEe4 e4 15.0 16.4
PEe5 e5 9.2 14.0
PEe6 e6 17.0 9.6
PEe7 e7 14.3 8.1
PEe8 e8 11.5 12.8
Total residual sum of squares rssTot: 3.357983
Residual Degrees of Freedom: 38
Multiple R-squared: 0.9954213
Fraction rss of rssTot per Experiment
Experiment rss perCent
1 e1 0.07 2.2
2 e2 0.26 7.8
3 e3 0.24 7.2
4 e4 0.11 3.2
5 e5 0.57 16.9
6 e6 1.25 37.2
7 e7 0.83 24.6
8 e8 0.03 1.0
method = ml
PEmethod = fix
dose dose2
-0.51079080 -0.02274661
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ml
PEmethod = fix
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.51079080 0.05783126 -8.832435 9.562192e-11
beta -0.02274661 0.01186134 -1.917710 6.268676e-02
Residual Deviance: 399.1192
Total residual sum of weighted squares rsswTot: 369.7449
Residual Degrees of Freedom: 38
Dispersion parameter: 9.730129
Fraction rssw of rsswTot per Experiment
Experiment rssw perCent
1 e1 6.39 1.7
2 e2 17.65 4.8
3 e3 43.57 11.8
4 e4 5.15 1.4
5 e5 109.36 29.6
6 e6 96.56 26.1
7 e7 86.86 23.5
8 e8 4.20 1.1
method = ls
PEmethod = fix
dose dose2
-0.53063032 -0.02331461
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = ls
PEmethod = fix
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.53063032 0.07510284 -7.065383 2.006471e-08
beta -0.02331461 0.01502057 -1.552179 1.289092e-01
Total residual sum of squares rssTot: 9.398594
Residual Degrees of Freedom: 38
Multiple R-squared: 0.9866913
Fraction rss of rssTot per Experiment
Experiment rss perCent
1 e1 0.14 1.5
2 e2 0.33 3.5
3 e3 1.01 10.7
4 e4 0.15 1.6
5 e5 1.57 16.7
6 e6 3.25 34.6
7 e7 2.85 30.4
8 e8 0.09 1.0
method = franken
PEmethod = fix
dose dose2
-0.4887937 -0.0219078
Use 'print' to see detailed results
*** Coefficients of LQ-model for cell survival ***
method = franken
PEmethod = fix
Shape parameters alpha and beta
Estimate Std. Error t value Pr(>|t|)
alpha -0.4887937 0.05385806 -9.075591 4.709574e-11
beta -0.0219078 0.01106990 -1.979043 5.509104e-02
Total residual sum of weighted squares rsswTot: 335.6884
Residual Degrees of Freedom: 38
Multiple R-squared: 0.9918373
Fraction rssw of rsswTot per Experiment
Experiment rssw perCent
1 e1 5.72 1.7
2 e2 11.98 3.6
3 e3 26.34 7.8
4 e4 5.23 1.6
5 e5 73.15 21.8
6 e6 107.79 32.1
7 e7 99.19 29.5
8 e8 6.28 1.9
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