summary-methods | R Documentation |
summary
Expands function summary
allowing printing summaries
objects of the class adpcr
to or
dpcr
.
object |
object of class |
print |
if |
The function prints a summary of the dPCR reaction, including k (number of positive chambers), n (total number of chambers), estimated lambda and concentration, as well as confidence intervals for the last two variables.
The data frame with estimated values of lambda, m and corresponding confidence intervals.
If summary is used on an object containing results of many
experiments, all experiments would be independently summarized. Currently
supported only for objects of class adpcr
.
Michal Burdukiewicz, Stefan Roediger.
Bhat S, Herrmann J, Corbisier P, Emslie K, Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number. Analytical and Bioanalytical Chemistry 2 (394), 2009.
Dube S, Qin J, Ramakrishnan R, Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device. PLoS ONE 3(8), 2008.
# array dpcr # Simulates a chamber based digital PCR with m total number of template molecules # and n number of chambers per plate and assigns it as object ptest of the class # adpcr for a single panel. The summary function on ptest gets assigned to summ # and the result with statistics according to Dube et al. 2008 and Bhat et al. 2009 # gets printed. ptest <- sim_adpcr(m = 400, n = 765, times = 5, dube = FALSE, n_panels = 1) summ <- summary(ptest) # save summary print(summ) # multiple experiments # Similar to the previous example but with five panels ptest <- sim_adpcr(m = 400, n = 765, times = 5, dube = FALSE, n_panels = 5) summary(ptest) # droplet dpcr - fluorescence # Simulates a droplet digital PCR with m = 7 total number of template molecules # and n = 20 number of droplets. The summary function on dropletf gives the # statistics according to Dube et al. 2008 and Bhat et al. 2009. The fluo parameter # is used to change the smoothness of the fluorescence curve and the space between # two consecutive measured peaks (droplets). dropletf <- sim_dpcr(m = 7, n = 20, times = 5, fluo = list(0.1, 0)) summary(dropletf) # droplet dpcr - number of molecules # Similar to the previous example but with five panels but without and modifications # to the peaks. droplet <- sim_dpcr(m = 7, n = 20, times = 5) summary(droplet) # Visualize the results of dropletf and dropletf # The curves of dropletf are smoother. par(mfrow = c(1, 2)) plot(dropletf, main = "With fluo parameter", type = "l") plot(droplet, main = "Without fluo parameter", type = "l")
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