modlist {qpcR} | R Documentation |
Simple function to create a list of nonlinear models from the columns of a qPCR dataframe.
Very handy if following functions should be applied to different qPCR models, i.e. by sapply
.
modlist(x, cyc = 1, fluo = 2:ncol(x), fct = l5(), opt = FALSE, norm = FALSE)
x |
a dataframe containing the qPCR data. |
cyc |
the column containing the cycle numbers, defaults to 1 . |
fluo |
the column(s) containing the raw fluorescence data. If not specified, all columns will be used. |
fct |
the function used for building the model, using the function lists from the 'drc' package. |
opt |
logical. Should model optimization take place? If TRUE , model selection is applied. |
norm |
logical. Should the raw data be normalized to within [0, 1] before model fitting? |
For a more detailed description of the functions see i.e. 'l5()'.
A list with each item containing the model from each column. A 'names' attribute containing the column name is attached to each model.
Andrej-Nikolai Spiess
### calculate efficiencies for each run in ### the 'reps' data ml <- modlist(reps, fct = l5()) effs <- sapply(ml, function(x) efficiency(x)$eff) print(effs) ### 'crossing points' for the first 3 runs ### using best model and normalization ml <- modlist(reps, fluo = 2:4, fct = l4(), opt = TRUE, norm = TRUE) cps <- sapply(ml, function(x) efficiency(x)$cpD2) print(cps)