A function to analyze plot the raw data from a BioRad droplet digital PCR
bioamp is a function to plot and analyze the amplitude data of a
BioRad droplet digital PCR experiment.
bioamp(data = data, amp_x = 1, amp_y = 2, cluster = 3, robust = TRUE, plot = TRUE, stat = TRUE, xlab = "Assay 1 Amplitude", ylab = "Assay 2 Amplitude", ...)
Arguments
- data
- object of class
whatcontaining the amplitude data. - amp_x
- is the first amplitude channel (x-axis).
- amp_y
- is the second amplitude channel (y-axis).
- cluster
- are the clusters of the plot. The number indicates the column of a table, which contains the cluster information.
- robust
- Is the method used to calculate the location (mean or median) and dispersion (standard deviation or median absolute deviation).
- plot
- logical, if
TRUE, the plot is printed. - stat
- logical, if
TRUE, the statistics of the droplet digital PCR experiment are calculated. - xlab
- x-label of the plot.
- ylab
- y-label of the plot.
- …
- other arguments passed to the
plotfunction (seeplot.defaultfor details).
Examples
par(mfrow = c(1,2)) bioamp(data = pds_raw[["A01"]], main = "Well A01", pch = 19)#> Cluster.1 Cluster.2 Cluster.3 Cluster.4 #> Counts Ch. 1 11.00000 3.00000 398.0000 11552.00000 #> Counts Ch. 2 11.00000 3.00000 398.0000 11552.00000 #> Location Ch. 1 553.69556 2026.70093 995.2142 590.94425 #> Location Ch. 2 1084.54590 995.84230 3694.3724 3676.18494 #> Dispersion Ch. 1 24.43643 80.47304 182.0612 51.25585 #> Dispersion Ch. 2 84.69588 32.88620 136.8308 115.59810bioamp(data = pds_raw[["A02"]], main = "Well A02", pch = 19)#> Cluster.1 Cluster.2 Cluster.3 Cluster.4 #> Counts Ch. 1 9781.00000 792.00000 38.0000 587.00000 #> Counts Ch. 2 9781.00000 792.00000 38.0000 587.00000 #> Location Ch. 1 579.75195 2016.80012 1427.3433 586.43384 #> Location Ch. 2 1015.20868 999.26620 3468.6197 3465.11963 #> Dispersion Ch. 1 40.21337 177.15604 352.1041 46.17048 #> Dispersion Ch. 2 50.94112 58.83233 183.7515 159.30630par(mfrow = c(1,1))
