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countfitteR package - an overview

Jarosław Chilimoniuk, Alicja Gosiewska, Jadwiga Słowik, Stefan Rödiger, Michał Burdukiewicz

2025-07-01

1 Introduction

countfitteR is a R package and shiny app designed to perform analysis of count data. This vignette covers important features and data sets of the app. We extended our automatized imaging platform Willitzki et al. (2012) for a multiparametric analysis of cell damage (DNA double strand breaks) Rödiger et al. (2018). Digital image analysis of the DSB biomarkers gamma H2AX was used to describe the alteration of the cell phenotype.

2 Data sets

# Load countfitteR package
library(countfitteR)

# Assign the csv file to filename
data("case_study")

processed_counts <- process_counts(case_study)

fit_counts(processed_counts, model = "all")

## $L3_AF_DMSO_B_10_FITC_pois
## $L3_AF_DMSO_B_10_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_DMSO_B_10_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_DMSO_B_10_FITC_pois$BIC
## [1] 4.65396
## 
## $L3_AF_DMSO_B_10_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_100_ETP_11_FITC_pois
## $L3_AF_100_ETP_11_FITC_pois$coefficients
## lambda 
##   2.32 
## 
## $L3_AF_100_ETP_11_FITC_pois$confint
##           lower    upper
## lambda 2.039876 2.638591
## 
## $L3_AF_100_ETP_11_FITC_pois$BIC
## [1] 898.1618
## 
## $L3_AF_100_ETP_11_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_100_ETP_12_FITC_pois
## $L3_AF_100_ETP_12_FITC_pois$coefficients
##   lambda 
## 3.215686 
## 
## $L3_AF_100_ETP_12_FITC_pois$confint
##           lower    upper
## lambda 2.885854 3.583216
## 
## $L3_AF_100_ETP_12_FITC_pois$BIC
## [1] 1008.888
## 
## $L3_AF_100_ETP_12_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_Med_C_13_FITC_pois
## $L3_AF_Med_C_13_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_Med_C_13_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_Med_C_13_FITC_pois$BIC
## [1] 4.624973
## 
## $L3_AF_Med_C_13_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_Med_C_14_FITC_pois
## $L3_AF_Med_C_14_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_Med_C_14_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_Med_C_14_FITC_pois$BIC
## [1] 4.691348
## 
## $L3_AF_Med_C_14_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_DMSo_C_15_FITC_pois
## $L3_AF_DMSo_C_15_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_DMSo_C_15_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_DMSo_C_15_FITC_pois$BIC
## [1] 4.624973
## 
## $L3_AF_DMSo_C_15_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_DMSO_C_16_FITC_pois
## $L3_AF_DMSO_C_16_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_DMSO_C_16_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_DMSO_C_16_FITC_pois$BIC
## [1] 4.624973
## 
## $L3_AF_DMSO_C_16_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_100_ETP_17_FITC_pois
## $L3_AF_100_ETP_17_FITC_pois$coefficients
##   lambda 
## 5.571429 
## 
## $L3_AF_100_ETP_17_FITC_pois$confint
##           lower    upper
## lambda 5.137759 6.041704
## 
## $L3_AF_100_ETP_17_FITC_pois$BIC
## [1] 1254.79
## 
## $L3_AF_100_ETP_17_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_100_ETP_18_FITC_pois
## $L3_AF_100_ETP_18_FITC_pois$coefficients
## lambda 
##   4.13 
## 
## $L3_AF_100_ETP_18_FITC_pois$confint
##           lower    upper
## lambda 3.750293 4.548152
## 
## $L3_AF_100_ETP_18_FITC_pois$BIC
## [1] 852.1981
## 
## $L3_AF_100_ETP_18_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_Med_D_19_FITC_pois
## $L3_AF_Med_D_19_FITC_pois$coefficients
##       lambda 
## 3.775135e-12 
## 
## $L3_AF_Med_D_19_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_Med_D_19_FITC_pois$BIC
## [1] 3.89182
## 
## $L3_AF_Med_D_19_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_Med_A_1_FITC_pois
## $L3_AF_Med_A_1_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_Med_A_1_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_Med_A_1_FITC_pois$BIC
## [1] 4.615121
## 
## $L3_AF_Med_A_1_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_Med_D_20_FITC_pois
## $L3_AF_Med_D_20_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_Med_D_20_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_Med_D_20_FITC_pois$BIC
## [1] 4.615121
## 
## $L3_AF_Med_D_20_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_DMSo_D_21_FITC_pois
## $L3_AF_DMSo_D_21_FITC_pois$coefficients
##     lambda 
## 0.03921569 
## 
## $L3_AF_DMSo_D_21_FITC_pois$confint
##             lower     upper
## lambda 0.01471861 0.1044847
## 
## $L3_AF_DMSo_D_21_FITC_pois$BIC
## [1] 44.89051
## 
## $L3_AF_DMSo_D_21_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_DMSO_D_22_FITC_pois
## $L3_AF_DMSO_D_22_FITC_pois$coefficients
##       lambda 
## 1.388794e-12 
## 
## $L3_AF_DMSO_D_22_FITC_pois$confint
##        lower upper
## lambda     0   Inf
## 
## $L3_AF_DMSO_D_22_FITC_pois$BIC
## [1] 4.65396
## 
## $L3_AF_DMSO_D_22_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_100_ETP_23_FITC_pois
## $L3_AF_100_ETP_23_FITC_pois$coefficients
##   lambda 
## 3.252427 
## 
## $L3_AF_100_ETP_23_FITC_pois$confint
##           lower    upper
## lambda 2.922143 3.620042
## 
## $L3_AF_100_ETP_23_FITC_pois$BIC
## [1] 904.4198
## 
## $L3_AF_100_ETP_23_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_100_ETP_24_FITC_pois
## $L3_AF_100_ETP_24_FITC_pois$coefficients
##   lambda 
## 4.122642 
## 
## $L3_AF_100_ETP_24_FITC_pois$confint
##           lower    upper
## lambda 3.753679 4.527871
## 
## $L3_AF_100_ETP_24_FITC_pois$BIC
## [1] 1069.925
## 
## $L3_AF_100_ETP_24_FITC_pois$model
## [1] "pois"
## 
## 
## $L3_AF_DMSO_B_10_FITC_zip
## $L3_AF_DMSO_B_10_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_B_10_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_B_10_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_DMSO_B_10_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_100_ETP_11_FITC_zip
## $L3_AF_100_ETP_11_FITC_zip$coefficients
##    lambda         r 
## 9.6660843 0.7599853 
## 
## $L3_AF_100_ETP_11_FITC_zip$confint
##            lower      upper
## lambda 8.4986398 10.9938989
## r      0.8336233  0.6667831
## 
## $L3_AF_100_ETP_11_FITC_zip$BIC
## [1] 350.7979
## 
## $L3_AF_100_ETP_11_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_100_ETP_12_FITC_zip
## $L3_AF_100_ETP_12_FITC_zip$coefficients
##    lambda         r 
## 9.6464351 0.6666451 
## 
## $L3_AF_100_ETP_12_FITC_zip$confint
##            lower      upper
## lambda 8.6567015 10.7493264
## r      0.7511469  0.5698801
## 
## $L3_AF_100_ETP_12_FITC_zip$BIC
## [1] 422.6681
## 
## $L3_AF_100_ETP_12_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_Med_C_13_FITC_zip
## $L3_AF_Med_C_13_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_C_13_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_C_13_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_Med_C_13_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_Med_C_14_FITC_zip
## $L3_AF_Med_C_14_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_C_14_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_C_14_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_Med_C_14_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_DMSo_C_15_FITC_zip
## $L3_AF_DMSo_C_15_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSo_C_15_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSo_C_15_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_DMSo_C_15_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_DMSO_C_16_FITC_zip
## $L3_AF_DMSO_C_16_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_C_16_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_C_16_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_DMSO_C_16_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_100_ETP_17_FITC_zip
## $L3_AF_100_ETP_17_FITC_zip$coefficients
##    lambda         r 
## 9.4347312 0.4094769 
## 
## $L3_AF_100_ETP_17_FITC_zip$confint
##            lower      upper
## lambda 8.7000833 10.2314139
## r      0.5057206  0.3197023
## 
## $L3_AF_100_ETP_17_FITC_zip$BIC
## [1] 785.1512
## 
## $L3_AF_100_ETP_17_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_100_ETP_18_FITC_zip
## $L3_AF_100_ETP_18_FITC_zip$coefficients
##   lambda        r 
## 7.240419 0.429591 
## 
## $L3_AF_100_ETP_18_FITC_zip$confint
##            lower     upper
## lambda 6.5730901 7.9754980
## r      0.5281578 0.3363081
## 
## $L3_AF_100_ETP_18_FITC_zip$BIC
## [1] 529.0745
## 
## $L3_AF_100_ETP_18_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_Med_D_19_FITC_zip
## $L3_AF_Med_D_19_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_D_19_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_D_19_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_Med_D_19_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_Med_A_1_FITC_zip
## $L3_AF_Med_A_1_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_A_1_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_A_1_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_Med_A_1_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_Med_D_20_FITC_zip
## $L3_AF_Med_D_20_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_D_20_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_D_20_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_Med_D_20_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_DMSo_D_21_FITC_zip
## $L3_AF_DMSo_D_21_FITC_zip$coefficients
##    lambda         r 
## 3.9206890 0.9899978 
## 
## $L3_AF_DMSo_D_21_FITC_zip$confint
##            lower      upper
## lambda 1.4119173 10.8871829
## r      0.9985954  0.9323372
## 
## $L3_AF_DMSo_D_21_FITC_zip$BIC
## [1] 23.71735
## 
## $L3_AF_DMSo_D_21_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_DMSO_D_22_FITC_zip
## $L3_AF_DMSO_D_22_FITC_zip$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_D_22_FITC_zip$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_D_22_FITC_zip$BIC
## [1] NA
## 
## $L3_AF_DMSO_D_22_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_100_ETP_23_FITC_zip
## $L3_AF_100_ETP_23_FITC_zip$coefficients
##    lambda         r 
## 7.2775775 0.5530893 
## 
## $L3_AF_100_ETP_23_FITC_zip$confint
##            lower     upper
## lambda 6.5367714 8.1023384
## r      0.6460777 0.4562321
## 
## $L3_AF_100_ETP_23_FITC_zip$BIC
## [1] 510.5238
## 
## $L3_AF_100_ETP_23_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_100_ETP_24_FITC_zip
## $L3_AF_100_ETP_24_FITC_zip$coefficients
##    lambda         r 
## 8.9171717 0.5376739 
## 
## $L3_AF_100_ETP_24_FITC_zip$confint
##           lower     upper
## lambda 8.118659 9.7942229
## r      0.630148 0.4425329
## 
## $L3_AF_100_ETP_24_FITC_zip$BIC
## [1] 546.5235
## 
## $L3_AF_100_ETP_24_FITC_zip$model
## [1] "zip"
## 
## 
## $L3_AF_DMSO_B_10_FITC_nb
## $L3_AF_DMSO_B_10_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_B_10_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_B_10_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_DMSO_B_10_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_100_ETP_11_FITC_nb
## $L3_AF_100_ETP_11_FITC_nb$coefficients
##     lambda      theta 
## 2.32000000 0.08621744 
## 
## $L3_AF_100_ETP_11_FITC_nb$confint
##         lower    upper
## lambda 1.1756 4.578429
## 
## $L3_AF_100_ETP_11_FITC_nb$BIC
## [1] 283.9301
## 
## $L3_AF_100_ETP_11_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_100_ETP_12_FITC_nb
## $L3_AF_100_ETP_12_FITC_nb$coefficients
##       lambda        theta 
##     3.215686 42652.987498 
## 
## $L3_AF_100_ETP_12_FITC_nb$confint
##           lower    upper
## lambda 2.885839 3.583234
## 
## $L3_AF_100_ETP_12_FITC_nb$BIC
## [1] 1013.438
## 
## $L3_AF_100_ETP_12_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_Med_C_13_FITC_nb
## $L3_AF_Med_C_13_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_C_13_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_C_13_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_Med_C_13_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_Med_C_14_FITC_nb
## $L3_AF_Med_C_14_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_C_14_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_C_14_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_Med_C_14_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_DMSo_C_15_FITC_nb
## $L3_AF_DMSo_C_15_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSo_C_15_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSo_C_15_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_DMSo_C_15_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_DMSO_C_16_FITC_nb
## $L3_AF_DMSO_C_16_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_C_16_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_C_16_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_DMSO_C_16_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_100_ETP_17_FITC_nb
## $L3_AF_100_ETP_17_FITC_nb$coefficients
##    lambda     theta 
## 5.5714286 0.3442529 
## 
## $L3_AF_100_ETP_17_FITC_nb$confint
##           lower    upper
## lambda 3.981797 7.795681
## 
## $L3_AF_100_ETP_17_FITC_nb$BIC
## [1] 555.458
## 
## $L3_AF_100_ETP_17_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_100_ETP_18_FITC_nb
## $L3_AF_100_ETP_18_FITC_nb$coefficients
##    lambda     theta 
## 4.1300000 0.3921204 
## 
## $L3_AF_100_ETP_18_FITC_nb$confint
##           lower    upper
## lambda 2.976535 5.730454
## 
## $L3_AF_100_ETP_18_FITC_nb$BIC
## [1] 490.2015
## 
## $L3_AF_100_ETP_18_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_Med_D_19_FITC_nb
## $L3_AF_Med_D_19_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_D_19_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_D_19_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_Med_D_19_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_Med_A_1_FITC_nb
## $L3_AF_Med_A_1_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_A_1_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_A_1_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_Med_A_1_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_Med_D_20_FITC_nb
## $L3_AF_Med_D_20_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_D_20_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_D_20_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_Med_D_20_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_DMSo_D_21_FITC_nb
## $L3_AF_DMSo_D_21_FITC_nb$coefficients
##       lambda        theta 
## 3.921569e-02 3.132226e+03 
## 
## $L3_AF_DMSo_D_21_FITC_nb$confint
##             lower     upper
## lambda 0.01471826 0.1044872
## 
## $L3_AF_DMSo_D_21_FITC_nb$BIC
## [1] 49.5117
## 
## $L3_AF_DMSo_D_21_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_DMSO_D_22_FITC_nb
## $L3_AF_DMSO_D_22_FITC_nb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_D_22_FITC_nb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_D_22_FITC_nb$BIC
## [1] NA
## 
## $L3_AF_DMSO_D_22_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_100_ETP_23_FITC_nb
## $L3_AF_100_ETP_23_FITC_nb$coefficients
##    lambda     theta 
## 3.2524272 0.2332405 
## 
## $L3_AF_100_ETP_23_FITC_nb$confint
##           lower  upper
## lambda 2.149926 4.9203
## 
## $L3_AF_100_ETP_23_FITC_nb$BIC
## [1] 426.6125
## 
## $L3_AF_100_ETP_23_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_100_ETP_24_FITC_nb
## $L3_AF_100_ETP_24_FITC_nb$coefficients
##    lambda     theta 
## 4.1226415 0.2386911 
## 
## $L3_AF_100_ETP_24_FITC_nb$confint
##           lower    upper
## lambda 2.761353 6.155017
## 
## $L3_AF_100_ETP_24_FITC_nb$BIC
## [1] 481.1145
## 
## $L3_AF_100_ETP_24_FITC_nb$model
## [1] "nb"
## 
## 
## $L3_AF_DMSO_B_10_FITC_zinb
## $L3_AF_DMSO_B_10_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_B_10_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_B_10_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_DMSO_B_10_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_100_ETP_11_FITC_zinb
## $L3_AF_100_ETP_11_FITC_zinb$coefficients
##    lambda     theta         r 
## 9.1831594 1.5462921 0.7473636 
## 
## $L3_AF_100_ETP_11_FITC_zinb$confint
##            lower      upper
## lambda 6.4023305 13.1718313
## r      0.8270573  0.6466367
## 
## $L3_AF_100_ETP_11_FITC_zinb$BIC
## [1] 277.5103
## 
## $L3_AF_100_ETP_11_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_100_ETP_12_FITC_zinb
## $L3_AF_100_ETP_12_FITC_zinb$coefficients
##    lambda     theta         r 
## 9.3744201 2.1000871 0.6569722 
## 
## $L3_AF_100_ETP_12_FITC_zinb$confint
##           lower      upper
## lambda 7.208861 12.1905177
## r      0.745087  0.5565278
## 
## $L3_AF_100_ETP_12_FITC_zinb$BIC
## [1] 358.827
## 
## $L3_AF_100_ETP_12_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_Med_C_13_FITC_zinb
## $L3_AF_Med_C_13_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_C_13_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_C_13_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_Med_C_13_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_Med_C_14_FITC_zinb
## $L3_AF_Med_C_14_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_C_14_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_C_14_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_Med_C_14_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_DMSo_C_15_FITC_zinb
## $L3_AF_DMSo_C_15_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSo_C_15_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSo_C_15_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_DMSo_C_15_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_DMSO_C_16_FITC_zinb
## $L3_AF_DMSO_C_16_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_C_16_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_C_16_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_DMSO_C_16_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_100_ETP_17_FITC_zinb
## $L3_AF_100_ETP_17_FITC_zinb$coefficients
##    lambda     theta         r 
## 8.5692769 1.0976189 0.3498196 
## 
## $L3_AF_100_ETP_17_FITC_zinb$confint
##            lower      upper
## lambda 6.5382573 11.2312048
## r      0.4788107  0.2396031
## 
## $L3_AF_100_ETP_17_FITC_zinb$BIC
## [1] 551.4754
## 
## $L3_AF_100_ETP_17_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_100_ETP_18_FITC_zinb
## $L3_AF_100_ETP_18_FITC_zinb$coefficients
##   lambda    theta        r 
## 6.965092 2.373989 0.407043 
## 
## $L3_AF_100_ETP_18_FITC_zinb$confint
##           lower     upper
## lambda 5.686007 8.5319122
## r      0.513995 0.3082315
## 
## $L3_AF_100_ETP_18_FITC_zinb$BIC
## [1] 476.3609
## 
## $L3_AF_100_ETP_18_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_Med_D_19_FITC_zinb
## $L3_AF_Med_D_19_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_D_19_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_D_19_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_Med_D_19_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_Med_A_1_FITC_zinb
## $L3_AF_Med_A_1_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_A_1_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_A_1_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_Med_A_1_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_Med_D_20_FITC_zinb
## $L3_AF_Med_D_20_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_Med_D_20_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_Med_D_20_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_Med_D_20_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_DMSo_D_21_FITC_zinb
## $L3_AF_DMSo_D_21_FITC_zinb$coefficients
##       lambda        theta            r 
## 3.920675e+00 5.844842e+04 9.899977e-01 
## 
## $L3_AF_DMSo_D_21_FITC_zinb$confint
##            lower     upper
## lambda 1.4118576 10.887564
## r      0.9985954  0.932337
## 
## $L3_AF_DMSo_D_21_FITC_zinb$BIC
## [1] 28.34238
## 
## $L3_AF_DMSo_D_21_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_DMSO_D_22_FITC_zinb
## $L3_AF_DMSO_D_22_FITC_zinb$coefficients
## lambda 
##     NA 
## 
## $L3_AF_DMSO_D_22_FITC_zinb$confint
##        lower upper
## lambda    NA    NA
## 
## $L3_AF_DMSO_D_22_FITC_zinb$BIC
## [1] NA
## 
## $L3_AF_DMSO_D_22_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_100_ETP_23_FITC_zinb
## $L3_AF_100_ETP_23_FITC_zinb$coefficients
##    lambda     theta         r 
## 6.4954122 1.1948827 0.4992731 
## 
## $L3_AF_100_ETP_23_FITC_zinb$confint
##            lower     upper
## lambda 4.7251026 8.9289869
## r      0.6239444 0.3746922
## 
## $L3_AF_100_ETP_23_FITC_zinb$BIC
## [1] 423.3666
## 
## $L3_AF_100_ETP_23_FITC_zinb$model
## [1] "zinb"
## 
## 
## $L3_AF_100_ETP_24_FITC_zinb
## $L3_AF_100_ETP_24_FITC_zinb$coefficients
##    lambda     theta         r 
## 8.6811121 2.3406866 0.5251021 
## 
## $L3_AF_100_ETP_24_FITC_zinb$confint
##            lower      upper
## lambda 7.0289472 10.7216209
## r      0.6216434  0.4266473
## 
## $L3_AF_100_ETP_24_FITC_zinb$BIC
## [1] 461.0089
## 
## $L3_AF_100_ETP_24_FITC_zinb$model
## [1] "zinb"

References

Reddig, Annika, Claudia E. Rübe, Stefan Rödiger, Peter Schierack, Dirk Reinhold, and Dirk Roggenbuck. 2018. “DNA Damage Assessment and Potential Applications in Laboratory Diagnostics and Precision Medicine.” Journal of Laboratory and Precision Medicine 3 (4). https://jlpm.amegroups.org/article/view/4305/html.

Rödiger, Stefan, Marius Liefold, Madeleine Ruhe, Mark Reinwald, Eberhard Beck, and P. Markus Deckert. 2018. “Quantification of DNA Double-Strand Breaks in Peripheral Blood Mononuclear Cells from Healthy Donors Exposed to Bendamustine by an Automated γH2AX Assay—an Exploratory Study.” Journal of Laboratory and Precision Medicine 3 (5). https://jlpm.amegroups.org/article/view/4370/html.

Rödiger, Stefan, Peter Schierack, Alexander Böhm, Jörg Nitschke, Ingo Berger, Ulrike Frömmel, Carsten Schmidt, et al. 2013. “A Highly Versatile Microscope Imaging Technology Platform for the Multiplex Real-Time Detection of Biomolecules and Autoimmune Antibodies.” Advances in Biochemical Engineering/Biotechnology 133: 35–74. https://doi.org/10.1007/10_2011_132.

Willitzki, Annika, Rico Hiemann, Vanessa Peters, Ulrich Sack, Peter Schierack, Stefan Rödiger, Ursula Anderer, et al. 2012. “New Platform Technology for Comprehensive Serological Diagnostics of Autoimmune Diseases.” Clinical & Developmental Immunology 2012: 284740. https://doi.org/10.1155/2012/284740.

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