Calculate dR/dT of melt curves for of every well in a plate.
Source:R/amp_melt_curve_functions.R
calculate_drdt_plate.RddR/dT, the derivative of the melt curve (of fluorescence signal R vs temperature T), has a maximum at the melting temperature Tm. A single peak in this suggests a single-length PCR product is present in the well.
Details
Note that this function does not group by plate, only by well. The function will give strange results if you pass it data from more than one plate. Avoid this by analysing one plate at a time.
See also
Other melt_curve_functions:
calculate_dydx()
Examples
# create simple curve
# create simple dataset of raw fluorescence with two samples
temp_tibble <- tibble(sample_id = rep(c("S1", "S2"), each = 10),
target_id = "T1",
well_row = "A",
well_col = rep(c(1, 2), each = 10),
well = rep(c("A1", "A2"), each = 10),
temperature = rep(56:65,2),
fluor_raw = c(1:10, 6:15))
# calculate drdt of all melt curves
#----- use case 1 : using splines
temp_tibble %>%
calculate_drdt_plate()
#> # A tibble: 20 × 8
#> sample_id target_id well_row well_col well temperature fluor_raw dRdT
#> <chr> <chr> <chr> <dbl> <chr> <int> <int> <dbl>
#> 1 S1 T1 A 1 A1 56 1 -1.00
#> 2 S1 T1 A 1 A1 57 2 -1
#> 3 S1 T1 A 1 A1 58 3 -1.00
#> 4 S1 T1 A 1 A1 59 4 -1.00
#> 5 S1 T1 A 1 A1 60 5 -1.00
#> 6 S1 T1 A 1 A1 61 6 -1.00
#> 7 S1 T1 A 1 A1 62 7 -1
#> 8 S1 T1 A 1 A1 63 8 -1.00
#> 9 S1 T1 A 1 A1 64 9 -1.00
#> 10 S1 T1 A 1 A1 65 10 -1.00
#> 11 S2 T1 A 2 A2 56 6 -1.00
#> 12 S2 T1 A 2 A2 57 7 -1
#> 13 S2 T1 A 2 A2 58 8 -1.00
#> 14 S2 T1 A 2 A2 59 9 -1.00
#> 15 S2 T1 A 2 A2 60 10 -1
#> 16 S2 T1 A 2 A2 61 11 -1.00
#> 17 S2 T1 A 2 A2 62 12 -1.00
#> 18 S2 T1 A 2 A2 63 13 -1.00
#> 19 S2 T1 A 2 A2 64 14 -1.00
#> 20 S2 T1 A 2 A2 65 15 -1.00
# optional arguments are passed to smooth.splines function
temp_tibble %>%
calculate_drdt_plate(spar = 0.5)
#> # A tibble: 20 × 8
#> sample_id target_id well_row well_col well temperature fluor_raw dRdT
#> <chr> <chr> <chr> <dbl> <chr> <int> <int> <dbl>
#> 1 S1 T1 A 1 A1 56 1 -1.00
#> 2 S1 T1 A 1 A1 57 2 -1.00
#> 3 S1 T1 A 1 A1 58 3 -1.00
#> 4 S1 T1 A 1 A1 59 4 -1.00
#> 5 S1 T1 A 1 A1 60 5 -1.00
#> 6 S1 T1 A 1 A1 61 6 -1.00
#> 7 S1 T1 A 1 A1 62 7 -1
#> 8 S1 T1 A 1 A1 63 8 -1.00
#> 9 S1 T1 A 1 A1 64 9 -1.00
#> 10 S1 T1 A 1 A1 65 10 -1.00
#> 11 S2 T1 A 2 A2 56 6 -1.00
#> 12 S2 T1 A 2 A2 57 7 -1.00
#> 13 S2 T1 A 2 A2 58 8 -1.00
#> 14 S2 T1 A 2 A2 59 9 -1.00
#> 15 S2 T1 A 2 A2 60 10 -1.00
#> 16 S2 T1 A 2 A2 61 11 -1.00
#> 17 S2 T1 A 2 A2 62 12 -1
#> 18 S2 T1 A 2 A2 63 13 -1.00
#> 19 S2 T1 A 2 A2 64 14 -1.00
#> 20 S2 T1 A 2 A2 65 15 -1.00
#----- use case 2 : using difference between adjacent points
temp_tibble %>%
calculate_drdt_plate(method = "diff")
#> # A tibble: 20 × 8
#> sample_id target_id well_row well_col well temperature fluor_raw dRdT
#> <chr> <chr> <chr> <dbl> <chr> <int> <int> <dbl>
#> 1 S1 T1 A 1 A1 56 1 -1
#> 2 S1 T1 A 1 A1 57 2 -1
#> 3 S1 T1 A 1 A1 58 3 -1
#> 4 S1 T1 A 1 A1 59 4 -1
#> 5 S1 T1 A 1 A1 60 5 -1
#> 6 S1 T1 A 1 A1 61 6 -1
#> 7 S1 T1 A 1 A1 62 7 -1
#> 8 S1 T1 A 1 A1 63 8 -1
#> 9 S1 T1 A 1 A1 64 9 -1
#> 10 S1 T1 A 1 A1 65 10 NA
#> 11 S2 T1 A 2 A2 56 6 -1
#> 12 S2 T1 A 2 A2 57 7 -1
#> 13 S2 T1 A 2 A2 58 8 -1
#> 14 S2 T1 A 2 A2 59 9 -1
#> 15 S2 T1 A 2 A2 60 10 -1
#> 16 S2 T1 A 2 A2 61 11 -1
#> 17 S2 T1 A 2 A2 62 12 -1
#> 18 S2 T1 A 2 A2 63 13 -1
#> 19 S2 T1 A 2 A2 64 14 -1
#> 20 S2 T1 A 2 A2 65 15 NA