[R] How to find quantitative cycle PCR with R?

[Luigi Marongiu]

Hello,
I would like to analyze quantitative PCR (qPCR) data using R rather
than proprietary softwares.
I can see there are several packages out there, but mostly they
perform relative quantification, while none provide a quantitative
cycle (Cq), or crossing over cycle.
Is there a package that can provide a Cq for a given threshold level?
Or is it possible to determine the value with regression?

I can fit a model on qPCR data using for instance the package qpcR
(https://cran.r-project.org/web/packages/qpcR/index.html):

```
val = c(120.64,    66.14,    34.87,    27.11,    8.87,    -5.8,
4.52,    -7.16,    -17.39,
        -14.29,    -20.26,    -14.99,    -21.05,    -20.64,    -8.03,
  -21.56,    -1.28,    15.01,
        75.26,    191.76,    455.09,    985.96,    1825.59,
2908.08,    3993.18,    5059.94,
        6071.93,    6986.32,    7796.01,    8502.25,    9111.46,
9638.01,    10077.19,
        10452.02,    10751.81,    11017.49,    11240.37,    11427.47,
  11570.07,    11684.96,
        11781.77,    11863.35,    11927.44,    11980.81,    12021.88,
  12058.35,    12100.63,
        12133.57,    12148.89,    12137.09)
x <- data.frame(Cycles = 1:35, val)
library(qpcR)
fit <- pcrfit(data=x,         # selected data
              cyc=1, fluo=2)  # columns for cycles and fluorescence
summary(fit)
```

The package allows the determination of a take-over point, but this is
the cycle where the data start moving into the exponential phase:
```
takeoff(fit, pval = 0.05, nsig = 3)
```
However, this level is too low; the Cq would probably be way higher on
the y-axis, and there are instances where I would like to use a
pre-fixed threshold value.

How can I determine a Cq with R?
Thank you

-- 
Best regards,
Luigi