bdChemo: Estimations of cell birth and death rates under drug...

In YiyiLiu1/bdChemo: Cell birth and death rates estimation

Estimations of cell birth and death rates under drug interventions

Description

Generate posterior estimations (mean and credible intervals) of dose-specific cell birth and death rates, and dose-response curve summary statistics GI_{50}, TGI and LC_{50}.

Usage

bdChemo(z, x0, xt, x0c, xtc, bk, curve.plot, sample.return,
N = 5e6, sa2l = .5, sa2m = 1, at = 10, bt = 1, al = 25, bl = 6,
ql = .025, qu = .975)

Arguments

z	compound concentrations (in \log_{10} scale); a vector
x0	initial cell population sizes corresponding to concentrations in z; a vector (same length as z)
xt	cell population sizes at follow-up time corresponding to concentrations in z; a vector (same length as z)
x0c	control group (without compound treatment) initial cell population size; a scaler (if there are replicates, take average); used only for computing GI50
xtc	control group (without compound treatment) cell population size at follow-up time; a scaler (if there are replicates, take average); used only for computing GI50
bk	background noise measurements; a vector
curve.plot	whether to produce cell growth, birth and death rates plots
sample.return	whether posterior samples of \lambda and \lambda should be returned
N	number of iterations;
sa2l	prior normal distribution variance for \alpha_\lambda; sa2l controls the scale of \phi_\lambda in prior;
sa2m	prior normal distribution variance for \alpha_\mu; controls the scale of \phi_\mu in prior;
at	prior inverse-gamma distribution shape parameter for \tau_\lambda^2 and \tau_\mu^2;
bt	prior inverse-gamma distribution rate parameter for \tau_\lambda^2 and \tau_\mu^2; at and bt together control the scale of \tau^2 in prior, which affects the fluctuation amplitude of the estimated curve (\tau is called amplitude parameter of the Gaussian kernel and the larger \tau^2 is, the larger the amplitude tends to be)
al	prior gamma distribution shape parameter for l_\lambda^2 and l_\mu^2
bl	prior gamma distribution rate parameter for l_\lambda^2 and l_\mu^2; al and bl together control the scale of l^2 in prior, which affects the smoothness of the estimated curve (l is called the length scale parameter of the Gaussian kernel, the larger l^2 is, the smoother the curve tends to be)
ql	lower bound of credible interval intended to output
qu	upper bound of credible interval intended to output

Value

A list with the following elements

znew	points where growth rates (means of Kendall Processes), birth and death rates are estimated
lambdas	posterior means and credible intervals of birth rate \lambda(z); a matrix (colums for different concentrations in znew)
mus	posterior means and credible intervals of death rate \mu(z); a matrix (colums for different concentrations in znew)
kmean	posterior means and credible intervals of growth rate (Kendal Process mean) m(z); a matrix (colums for different concentrations in znew)
summary	posterior means and credible intervals of GI_{50}, TGI, LC_{50}; a matrix (columns for different variables)
post.lambda	posterior samples of \lambda at znew, only returned if sample.return = T
post.mu	posterior samples of \mu at znew, only returned if sample.return = T

If "curve.plot" is T, also return plots of cell growth, birth and death estimations as shown in the main manuscript (curves and shades for mean and credible intervals, respectively)

Author(s)

Yiyi Liu

References

Liu Y. and Crawford F., Estimating dose-specific cell division and apoptosis rates from chemo-sensitivity experiments, submitted.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.
data(example)
bd.example = bdChemo(example$z, example$x0, example$xt,
example$x0c, example$xtc, example$bk, curve.plot = TRUE,
sample.return = FALSE, N = 1e5)

YiyiLiu1/bdChemo documentation built on May 8, 2023, 11:27 p.m.