encu.Rdencu (ENcode CUrves) is a function to calculate numerous
features of a large amplification curve data set.
The pcrfit_single is
performing the analysis for a single process.
encu(data, detection_chemistry = NA, device = NA)
| data | is the data set containing the cycles and fluorescence amplitudes. |
|---|---|
| detection_chemistry | contains additional meta information about the detection chemistry (e.g., probes, intercalating dye) that was used. |
| device | contains additional meta information about the qPCR system that was used. |
The output of the encu function is
identical to the pcrfit_single function.
# Calculate curve features of an amplification curve data. Note that not all # available CPU cores are used. If need set "all" to use all available cores. # In this example the testdat data set from the qpcR package is used. # The samples F1.1 and F1.2 are positive amplification curves. The samples # F1.3 and F1.4 are negative. library(qpcR) res_encu <- encu(testdat[, 1:3])#>#>res_encu#> runs cpD1 cpD2 cpD2_approx cpD2_ratio eff sliwin cpDdiff #> 1 F1.1 17.49 15.62 15.29714 1.021106 1.819425 1.739444 1.87 #> 2 F1.2 17.39 15.59 15.16525 1.028008 1.782711 1.737737 1.80 #> loglin_slope cpD2_range top f.top tdp f.tdp bg.stop amp.stop #> 1 0.1382870 4.527127 10 0.01391000 33 0.9830427 9 30 #> 2 0.1421122 4.496545 10 0.01330956 29 0.9889347 9 27 #> b_slope b_model_param c_model_param d_model_param e_model_param #> 1 -12.73839 -13.47658 0.003242222 0.9894974 18.24647 #> 2 -13.90384 -16.36373 0.002305736 0.9830211 18.46327 #> f_model_param f_intercept convInfo_iteratons qPCRmodel qPCRmodelRF #> 1 0.7304393 0.9283717 8 l7 l7 #> 2 0.5350400 0.7622996 8 l7 l7 #> minRFU maxRFU init2 fluo slope_bg intercept_bg #> 1 -0.004237230 1 1.700487e-05 0.1953197 0.001733801 -0.006777540 #> 2 -0.003998994 1 2.631616e-05 0.2160592 0.001635822 -0.006490719 #> sigma_bg sd_bg head2tail_ratio mblrr_slope_pt mblrr_intercept_bg #> 1 0.0002022220 0.4527011 -0.0007122453 -0.0003719424 -0.006442819 #> 2 0.0002437449 0.4453795 -0.0009850845 -0.0002171012 -0.006274295 #> mblrr_slope_bg mblrr_cor_bg mblrr_intercept_pt mblrr_cor_pt polyarea #> 1 0.001572672 0.9323391 1.008902 0 -0.1559269 #> 2 0.001548088 0.9198655 1.001047 0 -0.1684371 #> peaks_ratio autocorellation cp_e.agglo cp_bcp amptester_shapiro amptester_lrt #> 1 0.02584771 0.4994275 2 14 FALSE TRUE #> 2 0.03090811 0.4521168 2 12 FALSE TRUE #> amptester_rgt amptester_tht amptester_slt amptester_polygon #> 1 TRUE TRUE TRUE 4.742807 #> 2 TRUE TRUE TRUE 4.782519 #> amptester_slope.ratio hookreg_hook hookreg_hook_slope hookreg_hook_delta #> 1 0.2223128 1 -0.001613054 16 #> 2 0.2163902 1 -0.002352293 19 #> central_angle number_of_cycles detection_chemistry device #> 1 -0.9901063 49 NA NA #> 2 -0.9896863 49 NA NA