Case 1: Fibroblast

Datasource: Ref

This example data has been integrated in the SPARKLE (SPARKLE::cwas.test.data)

Input data

Input formats : Seurat metadata

library(SPARKLE)


Fibroblast.data <-SPARKLE::cwas.test.data

knitr::kable(head(Fibroblast.data), caption = "Seurat metadata")

Seurat metadata
Sample	Celltype	rate	Phenotype	Group	Subgroup	TGFB1	TGFB2	TGFB3
001C	MYO-F	0.1250000	Control	Lung	GSE136831	0.0000000	0.0000000	0.0000000
001C	PIF	0.8750000	Control	Lung	GSE136831	0.2109449	0.2418454	0.0000000
003C	APF2	0.2954545	Control	Lung	GSE136831	0.5165068	0.0000000	0.0585606
003C	FTF1	0.0454545	Control	Lung	GSE136831	0.1451997	0.0000000	0.8978785
003C	FTF2	0.0227273	Control	Lung	GSE136831	0.0000000	0.0000000	0.0000000
003C	MYO-F	0.0909091	Control	Lung	GSE136831	0.3260869	0.0000000	0.0000000

sparkle.data <-   cwas.test.data <-  cwas_build_model_data(inputdata = Fibroblast.data,
                                           Sample = "Sample", Phenotype = "Phenotype",
                                           Celltype = "Celltype",Group = "Group",Subgroup = "Subgroup",
                                           Control_label="Control",
                                           Disease_label="Disease",
                                           selected_celltype = c("MTF","MYO-F")
                                           )

## [1] "Warning: No Covariate1 infomation"
## [1] "Warning: No Covariate2 infomation"
## [1] "No gene infomation added"
## [1] "No geneset score infomation added"

Data exporlation (Optional)

PCA

PCA plot for data exploration

cwas_pcadraw(sparkle.data)

Wilcoxon

Wilcoxon rank sum test and plot

cwas_classic_comparision(sparkle.data)

Hausman_test

Test for Group

df <- cwas_hausman_test_all(sparkle.data,variable = "Group")


knitr::kable(df, caption = "Hausman test")

Hausman test
Celltype	Hausman_Statistic	Pvalue	Model_Selection	Varible
MYO_F	-19.10500	1	Random Effects Model	Group : Group
MTF	-10.75848	1	Random Effects Model	Group : Group

Test for Subgroup

df2 <- cwas_hausman_test_all(sparkle.data,variable = "Subgroup")

knitr::kable(df2, caption = "Hausman test")

Hausman test
Celltype	Hausman_Statistic	Pvalue	Model_Selection	Varible
MYO_F	0.6289437	0.7301744	Random Effects Model	Subgroup : Subgroup
MTF	-0.0845107	1.0000000	Random Effects Model	Subgroup : Subgroup

Cell-phenotype association analysis

All model calculation

all.models <- cwas_allmodel_cal(sparkle.data)### calculation for all model

Heatmap plot for all model

p <- cwas_allmodel_heatmap(all.models)# Plot all model AIC and Pvalue

Forest plot for Best model selection

best.model <- cwas_autoselected_model(all.models)# Select the best model and plot

Cell-phenotype covariate analysis

all.model.cov <- cwas_2celltype_allmodel_cal(sparkle.data)# Select the best model and plot
cwas_allmodel_heatmap(all.model.cov)# Plot all model AIC and Pvalue

best.model.cov <- cwas_autoselected_model(all.model.cov)# Select the best model and plot

Cell-phenotype mediation analysis

Your_interested_celltype="MTF"

all.model.med <- cwas_mediation_analysis(sparkle.data,X.cell = Your_interested_celltype,Best_model =best.model,method = "cell_mediate_cell" )# Select the best model and plot

Cell-phenotype moderation analysis

all.model.mod <- cwas_moderation_analysis(sparkle.data,X.cell =Your_interested_celltype,Best_model =best.model,method = "cell_moderation_cell" )# Select the best model and plot

Moderation network plot

sparkle.data <-   cwas.test.data <-  cwas_build_model_data(inputdata = Fibroblast.data,
                                           Sample = "Sample", Phenotype = "Phenotype",
                                           Celltype = "Celltype",Group = "Group",Subgroup = "Subgroup",
                                           Control_label="Control",
                                           Disease_label="Disease"
                                           )

SPARKLE::Cell_phenotype_network_plot(sparkle.data )

## [1] "285 Sample were enronlled in the model"
## [1] "group1 PIF fitting models have been calculated successful"
## [1] "group2 PIF fitting models have been calculated successful"
## [1] "group3 PIF fitting models have been calculated successful"
## [1] "group4 PIF fitting models have been calculated successful"
## [1] "24PIF fitting models have been calculated successful"
## [1] 1
## [1] "288 Sample were enronlled in the model"
## [1] "group1 MYO_F fitting models have been calculated successful"
## [1] "group2 MYO_F fitting models have been calculated successful"
## [1] "group3 MYO_F fitting models have been calculated successful"
## [1] "group4 MYO_F fitting models have been calculated successful"
## [1] "24MYO_F fitting models have been calculated successful"
## [1] 2
## [1] "93 Sample were enronlled in the model"
## [1] "group1 FTF1 fitting models have been calculated successful"
## [1] "group2 FTF1 fitting models have been calculated successful"
## [1] "group3 FTF1 fitting models have been calculated successful"
## [1] "group4 FTF1 fitting models have been calculated successful"
## [1] "20FTF1 fitting models have been calculated successful"
## [1] 3
## [1] "140 Sample were enronlled in the model"
## [1] "group1 FTF2 fitting models have been calculated successful"
## [1] "group2 FTF2 fitting models have been calculated successful"
## [1] "group3 FTF2 fitting models have been calculated successful"
## [1] "group4 FTF2 fitting models have been calculated successful"
## [1] "23FTF2 fitting models have been calculated successful"
## [1] 4
## [1] "220 Sample were enronlled in the model"
## [1] "group1 APF2 fitting models have been calculated successful"
## [1] "group2 APF2 fitting models have been calculated successful"
## [1] "group3 APF2 fitting models have been calculated successful"
## [1] "group4 APF2 fitting models have been calculated successful"
## [1] "20APF2 fitting models have been calculated successful"
## [1] 5
## [1] "179 Sample were enronlled in the model"
## [1] "group1 EMT_F fitting models have been calculated successful"
## [1] "group2 EMT_F fitting models have been calculated successful"
## [1] "group3 EMT_F fitting models have been calculated successful"
## [1] "group4 EMT_F fitting models have been calculated successful"
## [1] "24EMT_F fitting models have been calculated successful"
## [1] 6
## [1] "190 Sample were enronlled in the model"
## [1] "group1 MTF fitting models have been calculated successful"
## [1] "group2 MTF fitting models have been calculated successful"
## [1] "group3 MTF fitting models have been calculated successful"
## [1] "group4 MTF fitting models have been calculated successful"
## [1] "22MTF fitting models have been calculated successful"
## [1] 7
## [1] "149 Sample were enronlled in the model"
## [1] "group1 APF1 fitting models have been calculated successful"
## [1] "group2 APF1 fitting models have been calculated successful"
## [1] "group3 APF1 fitting models have been calculated successful"
## [1] "group4 APF1 fitting models have been calculated successful"
## [1] "22APF1 fitting models have been calculated successful"
## [1] 8
## [1] "31 Sample were enronlled in the model"
## [1] "group1 MSC_F fitting models have been calculated successful"
## [1] "group2 MSC_F fitting models have been calculated successful"
## [1] "group3 MSC_F fitting models have been calculated successful"
## [1] "group4 MSC_F fitting models have been calculated successful"
## [1] "24MSC_F fitting models have been calculated successful"
## [1] 9
## [1] "All models Selection"
## significant model selected
## [1] 1
## significant model selected
## [1] 2
## significant model selected
## [1] 3
## no significant model
## [1] 4
## no significant model
## [1] 5
## no significant model
## [1] 6
## significant model selected
## [1] 7
## significant model selected
## [1] 8
## no significant model
## [1] 9
## [1] "Warning Message: No Adjusted p value in this data"

## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 APF2 interactionfitting models have been calculated successful"
## [1] "group2 APF1 APF2 interactionfitting models have been calculated successful"
## [1] "group3 APF1 APF2 interactionfitting models have been calculated successful"
## [1] "group4 APF1 APF2 interactionfitting models have been calculated successful"
## [1] "24APF1 APF2 interactionfitting models have been calculated successful"
## [1] 1
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 EMT_F interactionfitting models have been calculated successful"
## [1] "group2 APF1 EMT_F interactionfitting models have been calculated successful"
## [1] "group3 APF1 EMT_F interactionfitting models have been calculated successful"
## [1] "group4 APF1 EMT_F interactionfitting models have been calculated successful"
## [1] "24APF1 EMT_F interactionfitting models have been calculated successful"
## [1] 2
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 FTF1 interactionfitting models have been calculated successful"
## [1] "group2 APF1 FTF1 interactionfitting models have been calculated successful"
## [1] "group3 APF1 FTF1 interactionfitting models have been calculated successful"
## [1] "group4 APF1 FTF1 interactionfitting models have been calculated successful"
## [1] "24APF1 FTF1 interactionfitting models have been calculated successful"
## [1] 3
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 FTF2 interactionfitting models have been calculated successful"
## [1] "group2 APF1 FTF2 interactionfitting models have been calculated successful"
## [1] "group3 APF1 FTF2 interactionfitting models have been calculated successful"
## [1] "group4 APF1 FTF2 interactionfitting models have been calculated successful"
## [1] "24APF1 FTF2 interactionfitting models have been calculated successful"
## [1] 4
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 MSC_F interactionfitting models have been calculated successful"
## [1] "group2 APF1 MSC_F interactionfitting models have been calculated successful"
## [1] "group3 APF1 MSC_F interactionfitting models have been calculated successful"
## [1] "group4 APF1 MSC_F interactionfitting models have been calculated successful"
## [1] "24APF1 MSC_F interactionfitting models have been calculated successful"
## [1] 5
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 MTF interactionfitting models have been calculated successful"
## [1] "group2 APF1 MTF interactionfitting models have been calculated successful"
## [1] "group3 APF1 MTF interactionfitting models have been calculated successful"
## [1] "group4 APF1 MTF interactionfitting models have been calculated successful"
## [1] "24APF1 MTF interactionfitting models have been calculated successful"
## [1] 6
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 MYO_F interactionfitting models have been calculated successful"
## [1] "group2 APF1 MYO_F interactionfitting models have been calculated successful"
## [1] "group3 APF1 MYO_F interactionfitting models have been calculated successful"
## [1] "group4 APF1 MYO_F interactionfitting models have been calculated successful"
## [1] "24APF1 MYO_F interactionfitting models have been calculated successful"
## [1] 7
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF1 PIF interactionfitting models have been calculated successful"
## [1] "group2 APF1 PIF interactionfitting models have been calculated successful"
## [1] "group3 APF1 PIF interactionfitting models have been calculated successful"
## [1] "group4 APF1 PIF interactionfitting models have been calculated successful"
## [1] "24APF1 PIF interactionfitting models have been calculated successful"
## [1] 8
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 APF1 interactionfitting models have been calculated successful"
## [1] "group2 APF2 APF1 interactionfitting models have been calculated successful"
## [1] "group3 APF2 APF1 interactionfitting models have been calculated successful"
## [1] "group4 APF2 APF1 interactionfitting models have been calculated successful"
## [1] "24APF2 APF1 interactionfitting models have been calculated successful"
## [1] 9
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 EMT_F interactionfitting models have been calculated successful"
## [1] "group2 APF2 EMT_F interactionfitting models have been calculated successful"
## [1] "group3 APF2 EMT_F interactionfitting models have been calculated successful"
## [1] "group4 APF2 EMT_F interactionfitting models have been calculated successful"
## [1] "24APF2 EMT_F interactionfitting models have been calculated successful"
## [1] 10
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 FTF1 interactionfitting models have been calculated successful"
## [1] "group2 APF2 FTF1 interactionfitting models have been calculated successful"
## [1] "group3 APF2 FTF1 interactionfitting models have been calculated successful"
## [1] "group4 APF2 FTF1 interactionfitting models have been calculated successful"
## [1] "24APF2 FTF1 interactionfitting models have been calculated successful"
## [1] 11
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 FTF2 interactionfitting models have been calculated successful"
## [1] "group2 APF2 FTF2 interactionfitting models have been calculated successful"
## [1] "group3 APF2 FTF2 interactionfitting models have been calculated successful"
## [1] "group4 APF2 FTF2 interactionfitting models have been calculated successful"
## [1] "24APF2 FTF2 interactionfitting models have been calculated successful"
## [1] 12
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 MSC_F interactionfitting models have been calculated successful"
## [1] "group2 APF2 MSC_F interactionfitting models have been calculated successful"
## [1] "group3 APF2 MSC_F interactionfitting models have been calculated successful"
## [1] "group4 APF2 MSC_F interactionfitting models have been calculated successful"
## [1] "24APF2 MSC_F interactionfitting models have been calculated successful"
## [1] 13
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 MTF interactionfitting models have been calculated successful"
## [1] "group2 APF2 MTF interactionfitting models have been calculated successful"
## [1] "group3 APF2 MTF interactionfitting models have been calculated successful"
## [1] "group4 APF2 MTF interactionfitting models have been calculated successful"
## [1] "24APF2 MTF interactionfitting models have been calculated successful"
## [1] 14
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 MYO_F interactionfitting models have been calculated successful"
## [1] "group2 APF2 MYO_F interactionfitting models have been calculated successful"
## [1] "group3 APF2 MYO_F interactionfitting models have been calculated successful"
## [1] "group4 APF2 MYO_F interactionfitting models have been calculated successful"
## [1] "24APF2 MYO_F interactionfitting models have been calculated successful"
## [1] 15
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 APF2 PIF interactionfitting models have been calculated successful"
## [1] "group2 APF2 PIF interactionfitting models have been calculated successful"
## [1] "group3 APF2 PIF interactionfitting models have been calculated successful"
## [1] "group4 APF2 PIF interactionfitting models have been calculated successful"
## [1] "24APF2 PIF interactionfitting models have been calculated successful"
## [1] 16
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F APF1 interactionfitting models have been calculated successful"
## [1] "group2 EMT_F APF1 interactionfitting models have been calculated successful"
## [1] "group3 EMT_F APF1 interactionfitting models have been calculated successful"
## [1] "group4 EMT_F APF1 interactionfitting models have been calculated successful"
## [1] "24EMT_F APF1 interactionfitting models have been calculated successful"
## [1] 17
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F APF2 interactionfitting models have been calculated successful"
## [1] "group2 EMT_F APF2 interactionfitting models have been calculated successful"
## [1] "group3 EMT_F APF2 interactionfitting models have been calculated successful"
## [1] "group4 EMT_F APF2 interactionfitting models have been calculated successful"
## [1] "24EMT_F APF2 interactionfitting models have been calculated successful"
## [1] 18
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F FTF1 interactionfitting models have been calculated successful"
## [1] "group2 EMT_F FTF1 interactionfitting models have been calculated successful"
## [1] "group3 EMT_F FTF1 interactionfitting models have been calculated successful"
## [1] "group4 EMT_F FTF1 interactionfitting models have been calculated successful"
## [1] "24EMT_F FTF1 interactionfitting models have been calculated successful"
## [1] 19
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F FTF2 interactionfitting models have been calculated successful"
## [1] "group2 EMT_F FTF2 interactionfitting models have been calculated successful"
## [1] "group3 EMT_F FTF2 interactionfitting models have been calculated successful"
## [1] "group4 EMT_F FTF2 interactionfitting models have been calculated successful"
## [1] "24EMT_F FTF2 interactionfitting models have been calculated successful"
## [1] 20
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F MSC_F interactionfitting models have been calculated successful"
## [1] "group2 EMT_F MSC_F interactionfitting models have been calculated successful"
## [1] "group3 EMT_F MSC_F interactionfitting models have been calculated successful"
## [1] "group4 EMT_F MSC_F interactionfitting models have been calculated successful"
## [1] "24EMT_F MSC_F interactionfitting models have been calculated successful"
## [1] 21
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F MTF interactionfitting models have been calculated successful"
## [1] "group2 EMT_F MTF interactionfitting models have been calculated successful"
## [1] "group3 EMT_F MTF interactionfitting models have been calculated successful"
## [1] "group4 EMT_F MTF interactionfitting models have been calculated successful"
## [1] "24EMT_F MTF interactionfitting models have been calculated successful"
## [1] 22
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F MYO_F interactionfitting models have been calculated successful"
## [1] "group2 EMT_F MYO_F interactionfitting models have been calculated successful"
## [1] "group3 EMT_F MYO_F interactionfitting models have been calculated successful"
## [1] "group4 EMT_F MYO_F interactionfitting models have been calculated successful"
## [1] "24EMT_F MYO_F interactionfitting models have been calculated successful"
## [1] 23
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 EMT_F PIF interactionfitting models have been calculated successful"
## [1] "group2 EMT_F PIF interactionfitting models have been calculated successful"
## [1] "group3 EMT_F PIF interactionfitting models have been calculated successful"
## [1] "group4 EMT_F PIF interactionfitting models have been calculated successful"
## [1] "24EMT_F PIF interactionfitting models have been calculated successful"
## [1] 24
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 APF1 interactionfitting models have been calculated successful"
## [1] "group2 FTF1 APF1 interactionfitting models have been calculated successful"
## [1] "group3 FTF1 APF1 interactionfitting models have been calculated successful"
## [1] "group4 FTF1 APF1 interactionfitting models have been calculated successful"
## [1] "24FTF1 APF1 interactionfitting models have been calculated successful"
## [1] 25
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 APF2 interactionfitting models have been calculated successful"
## [1] "group2 FTF1 APF2 interactionfitting models have been calculated successful"
## [1] "group3 FTF1 APF2 interactionfitting models have been calculated successful"
## [1] "group4 FTF1 APF2 interactionfitting models have been calculated successful"
## [1] "24FTF1 APF2 interactionfitting models have been calculated successful"
## [1] 26
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 EMT_F interactionfitting models have been calculated successful"
## [1] "group2 FTF1 EMT_F interactionfitting models have been calculated successful"
## [1] "group3 FTF1 EMT_F interactionfitting models have been calculated successful"
## [1] "group4 FTF1 EMT_F interactionfitting models have been calculated successful"
## [1] "24FTF1 EMT_F interactionfitting models have been calculated successful"
## [1] 27
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 FTF2 interactionfitting models have been calculated successful"
## [1] "group2 FTF1 FTF2 interactionfitting models have been calculated successful"
## [1] "group3 FTF1 FTF2 interactionfitting models have been calculated successful"
## [1] "group4 FTF1 FTF2 interactionfitting models have been calculated successful"
## [1] "24FTF1 FTF2 interactionfitting models have been calculated successful"
## [1] 28
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 MSC_F interactionfitting models have been calculated successful"
## [1] "group2 FTF1 MSC_F interactionfitting models have been calculated successful"
## [1] "group3 FTF1 MSC_F interactionfitting models have been calculated successful"
## [1] "group4 FTF1 MSC_F interactionfitting models have been calculated successful"
## [1] "24FTF1 MSC_F interactionfitting models have been calculated successful"
## [1] 29
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 MTF interactionfitting models have been calculated successful"
## [1] "group2 FTF1 MTF interactionfitting models have been calculated successful"
## [1] "group3 FTF1 MTF interactionfitting models have been calculated successful"
## [1] "group4 FTF1 MTF interactionfitting models have been calculated successful"
## [1] "24FTF1 MTF interactionfitting models have been calculated successful"
## [1] 30
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 MYO_F interactionfitting models have been calculated successful"
## [1] "group2 FTF1 MYO_F interactionfitting models have been calculated successful"
## [1] "group3 FTF1 MYO_F interactionfitting models have been calculated successful"
## [1] "group4 FTF1 MYO_F interactionfitting models have been calculated successful"
## [1] "24FTF1 MYO_F interactionfitting models have been calculated successful"
## [1] 31
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF1 PIF interactionfitting models have been calculated successful"
## [1] "group2 FTF1 PIF interactionfitting models have been calculated successful"
## [1] "group3 FTF1 PIF interactionfitting models have been calculated successful"
## [1] "group4 FTF1 PIF interactionfitting models have been calculated successful"
## [1] "24FTF1 PIF interactionfitting models have been calculated successful"
## [1] 32
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 APF1 interactionfitting models have been calculated successful"
## [1] "group2 FTF2 APF1 interactionfitting models have been calculated successful"
## [1] "group3 FTF2 APF1 interactionfitting models have been calculated successful"
## [1] "group4 FTF2 APF1 interactionfitting models have been calculated successful"
## [1] "24FTF2 APF1 interactionfitting models have been calculated successful"
## [1] 33
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 APF2 interactionfitting models have been calculated successful"
## [1] "group2 FTF2 APF2 interactionfitting models have been calculated successful"
## [1] "group3 FTF2 APF2 interactionfitting models have been calculated successful"
## [1] "group4 FTF2 APF2 interactionfitting models have been calculated successful"
## [1] "24FTF2 APF2 interactionfitting models have been calculated successful"
## [1] 34
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 EMT_F interactionfitting models have been calculated successful"
## [1] "group2 FTF2 EMT_F interactionfitting models have been calculated successful"
## [1] "group3 FTF2 EMT_F interactionfitting models have been calculated successful"
## [1] "group4 FTF2 EMT_F interactionfitting models have been calculated successful"
## [1] "24FTF2 EMT_F interactionfitting models have been calculated successful"
## [1] 35
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 FTF1 interactionfitting models have been calculated successful"
## [1] "group2 FTF2 FTF1 interactionfitting models have been calculated successful"
## [1] "group3 FTF2 FTF1 interactionfitting models have been calculated successful"
## [1] "group4 FTF2 FTF1 interactionfitting models have been calculated successful"
## [1] "24FTF2 FTF1 interactionfitting models have been calculated successful"
## [1] 36
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 MSC_F interactionfitting models have been calculated successful"
## [1] "group2 FTF2 MSC_F interactionfitting models have been calculated successful"
## [1] "group3 FTF2 MSC_F interactionfitting models have been calculated successful"
## [1] "group4 FTF2 MSC_F interactionfitting models have been calculated successful"
## [1] "24FTF2 MSC_F interactionfitting models have been calculated successful"
## [1] 37
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 MTF interactionfitting models have been calculated successful"
## [1] "group2 FTF2 MTF interactionfitting models have been calculated successful"
## [1] "group3 FTF2 MTF interactionfitting models have been calculated successful"
## [1] "group4 FTF2 MTF interactionfitting models have been calculated successful"
## [1] "24FTF2 MTF interactionfitting models have been calculated successful"
## [1] 38
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 MYO_F interactionfitting models have been calculated successful"
## [1] "group2 FTF2 MYO_F interactionfitting models have been calculated successful"
## [1] "group3 FTF2 MYO_F interactionfitting models have been calculated successful"
## [1] "group4 FTF2 MYO_F interactionfitting models have been calculated successful"
## [1] "24FTF2 MYO_F interactionfitting models have been calculated successful"
## [1] 39
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 FTF2 PIF interactionfitting models have been calculated successful"
## [1] "group2 FTF2 PIF interactionfitting models have been calculated successful"
## [1] "group3 FTF2 PIF interactionfitting models have been calculated successful"
## [1] "group4 FTF2 PIF interactionfitting models have been calculated successful"
## [1] "24FTF2 PIF interactionfitting models have been calculated successful"
## [1] 40
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F APF1 interactionfitting models have been calculated successful"
## [1] "group2 MSC_F APF1 interactionfitting models have been calculated successful"
## [1] "group3 MSC_F APF1 interactionfitting models have been calculated successful"
## [1] "group4 MSC_F APF1 interactionfitting models have been calculated successful"
## [1] "24MSC_F APF1 interactionfitting models have been calculated successful"
## [1] 41
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F APF2 interactionfitting models have been calculated successful"
## [1] "group2 MSC_F APF2 interactionfitting models have been calculated successful"
## [1] "group3 MSC_F APF2 interactionfitting models have been calculated successful"
## [1] "group4 MSC_F APF2 interactionfitting models have been calculated successful"
## [1] "24MSC_F APF2 interactionfitting models have been calculated successful"
## [1] 42
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F EMT_F interactionfitting models have been calculated successful"
## [1] "group2 MSC_F EMT_F interactionfitting models have been calculated successful"
## [1] "group3 MSC_F EMT_F interactionfitting models have been calculated successful"
## [1] "group4 MSC_F EMT_F interactionfitting models have been calculated successful"
## [1] "24MSC_F EMT_F interactionfitting models have been calculated successful"
## [1] 43
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F FTF1 interactionfitting models have been calculated successful"
## [1] "group2 MSC_F FTF1 interactionfitting models have been calculated successful"
## [1] "group3 MSC_F FTF1 interactionfitting models have been calculated successful"
## [1] "group4 MSC_F FTF1 interactionfitting models have been calculated successful"
## [1] "24MSC_F FTF1 interactionfitting models have been calculated successful"
## [1] 44
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F FTF2 interactionfitting models have been calculated successful"
## [1] "group2 MSC_F FTF2 interactionfitting models have been calculated successful"
## [1] "group3 MSC_F FTF2 interactionfitting models have been calculated successful"
## [1] "group4 MSC_F FTF2 interactionfitting models have been calculated successful"
## [1] "24MSC_F FTF2 interactionfitting models have been calculated successful"
## [1] 45
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F MTF interactionfitting models have been calculated successful"
## [1] "group2 MSC_F MTF interactionfitting models have been calculated successful"
## [1] "group3 MSC_F MTF interactionfitting models have been calculated successful"
## [1] "group4 MSC_F MTF interactionfitting models have been calculated successful"
## [1] "24MSC_F MTF interactionfitting models have been calculated successful"
## [1] 46
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F MYO_F interactionfitting models have been calculated successful"
## [1] "group2 MSC_F MYO_F interactionfitting models have been calculated successful"
## [1] "group3 MSC_F MYO_F interactionfitting models have been calculated successful"
## [1] "group4 MSC_F MYO_F interactionfitting models have been calculated successful"
## [1] "24MSC_F MYO_F interactionfitting models have been calculated successful"
## [1] 47
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MSC_F PIF interactionfitting models have been calculated successful"
## [1] "group2 MSC_F PIF interactionfitting models have been calculated successful"
## [1] "group3 MSC_F PIF interactionfitting models have been calculated successful"
## [1] "group4 MSC_F PIF interactionfitting models have been calculated successful"
## [1] "24MSC_F PIF interactionfitting models have been calculated successful"
## [1] 48
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF APF1 interactionfitting models have been calculated successful"
## [1] "group2 MTF APF1 interactionfitting models have been calculated successful"
## [1] "group3 MTF APF1 interactionfitting models have been calculated successful"
## [1] "group4 MTF APF1 interactionfitting models have been calculated successful"
## [1] "24MTF APF1 interactionfitting models have been calculated successful"
## [1] 49
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF APF2 interactionfitting models have been calculated successful"
## [1] "group2 MTF APF2 interactionfitting models have been calculated successful"
## [1] "group3 MTF APF2 interactionfitting models have been calculated successful"
## [1] "group4 MTF APF2 interactionfitting models have been calculated successful"
## [1] "24MTF APF2 interactionfitting models have been calculated successful"
## [1] 50
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF EMT_F interactionfitting models have been calculated successful"
## [1] "group2 MTF EMT_F interactionfitting models have been calculated successful"
## [1] "group3 MTF EMT_F interactionfitting models have been calculated successful"
## [1] "group4 MTF EMT_F interactionfitting models have been calculated successful"
## [1] "24MTF EMT_F interactionfitting models have been calculated successful"
## [1] 51
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF FTF1 interactionfitting models have been calculated successful"
## [1] "group2 MTF FTF1 interactionfitting models have been calculated successful"
## [1] "group3 MTF FTF1 interactionfitting models have been calculated successful"
## [1] "group4 MTF FTF1 interactionfitting models have been calculated successful"
## [1] "24MTF FTF1 interactionfitting models have been calculated successful"
## [1] 52
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF FTF2 interactionfitting models have been calculated successful"
## [1] "group2 MTF FTF2 interactionfitting models have been calculated successful"
## [1] "group3 MTF FTF2 interactionfitting models have been calculated successful"
## [1] "group4 MTF FTF2 interactionfitting models have been calculated successful"
## [1] "24MTF FTF2 interactionfitting models have been calculated successful"
## [1] 53
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF MSC_F interactionfitting models have been calculated successful"
## [1] "group2 MTF MSC_F interactionfitting models have been calculated successful"
## [1] "group3 MTF MSC_F interactionfitting models have been calculated successful"
## [1] "group4 MTF MSC_F interactionfitting models have been calculated successful"
## [1] "24MTF MSC_F interactionfitting models have been calculated successful"
## [1] 54
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF MYO_F interactionfitting models have been calculated successful"
## [1] "group2 MTF MYO_F interactionfitting models have been calculated successful"
## [1] "group3 MTF MYO_F interactionfitting models have been calculated successful"
## [1] "group4 MTF MYO_F interactionfitting models have been calculated successful"
## [1] "24MTF MYO_F interactionfitting models have been calculated successful"
## [1] 55
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MTF PIF interactionfitting models have been calculated successful"
## [1] "group2 MTF PIF interactionfitting models have been calculated successful"
## [1] "group3 MTF PIF interactionfitting models have been calculated successful"
## [1] "group4 MTF PIF interactionfitting models have been calculated successful"
## [1] "24MTF PIF interactionfitting models have been calculated successful"
## [1] 56
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F APF1 interactionfitting models have been calculated successful"
## [1] "group2 MYO_F APF1 interactionfitting models have been calculated successful"
## [1] "group3 MYO_F APF1 interactionfitting models have been calculated successful"
## [1] "group4 MYO_F APF1 interactionfitting models have been calculated successful"
## [1] "24MYO_F APF1 interactionfitting models have been calculated successful"
## [1] 57
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F APF2 interactionfitting models have been calculated successful"
## [1] "group2 MYO_F APF2 interactionfitting models have been calculated successful"
## [1] "group3 MYO_F APF2 interactionfitting models have been calculated successful"
## [1] "group4 MYO_F APF2 interactionfitting models have been calculated successful"
## [1] "24MYO_F APF2 interactionfitting models have been calculated successful"
## [1] 58
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F EMT_F interactionfitting models have been calculated successful"
## [1] "group2 MYO_F EMT_F interactionfitting models have been calculated successful"
## [1] "group3 MYO_F EMT_F interactionfitting models have been calculated successful"
## [1] "group4 MYO_F EMT_F interactionfitting models have been calculated successful"
## [1] "24MYO_F EMT_F interactionfitting models have been calculated successful"
## [1] 59
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F FTF1 interactionfitting models have been calculated successful"
## [1] "group2 MYO_F FTF1 interactionfitting models have been calculated successful"
## [1] "group3 MYO_F FTF1 interactionfitting models have been calculated successful"
## [1] "group4 MYO_F FTF1 interactionfitting models have been calculated successful"
## [1] "24MYO_F FTF1 interactionfitting models have been calculated successful"
## [1] 60
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F FTF2 interactionfitting models have been calculated successful"
## [1] "group2 MYO_F FTF2 interactionfitting models have been calculated successful"
## [1] "group3 MYO_F FTF2 interactionfitting models have been calculated successful"
## [1] "group4 MYO_F FTF2 interactionfitting models have been calculated successful"
## [1] "24MYO_F FTF2 interactionfitting models have been calculated successful"
## [1] 61
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F MSC_F interactionfitting models have been calculated successful"
## [1] "group2 MYO_F MSC_F interactionfitting models have been calculated successful"
## [1] "group3 MYO_F MSC_F interactionfitting models have been calculated successful"
## [1] "group4 MYO_F MSC_F interactionfitting models have been calculated successful"
## [1] "24MYO_F MSC_F interactionfitting models have been calculated successful"
## [1] 62
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F MTF interactionfitting models have been calculated successful"
## [1] "group2 MYO_F MTF interactionfitting models have been calculated successful"
## [1] "group3 MYO_F MTF interactionfitting models have been calculated successful"
## [1] "group4 MYO_F MTF interactionfitting models have been calculated successful"
## [1] "24MYO_F MTF interactionfitting models have been calculated successful"
## [1] 63
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 MYO_F PIF interactionfitting models have been calculated successful"
## [1] "group2 MYO_F PIF interactionfitting models have been calculated successful"
## [1] "group3 MYO_F PIF interactionfitting models have been calculated successful"
## [1] "group4 MYO_F PIF interactionfitting models have been calculated successful"
## [1] "24MYO_F PIF interactionfitting models have been calculated successful"
## [1] 64
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF APF1 interactionfitting models have been calculated successful"
## [1] "group2 PIF APF1 interactionfitting models have been calculated successful"
## [1] "group3 PIF APF1 interactionfitting models have been calculated successful"
## [1] "group4 PIF APF1 interactionfitting models have been calculated successful"
## [1] "24PIF APF1 interactionfitting models have been calculated successful"
## [1] 65
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF APF2 interactionfitting models have been calculated successful"
## [1] "group2 PIF APF2 interactionfitting models have been calculated successful"
## [1] "group3 PIF APF2 interactionfitting models have been calculated successful"
## [1] "group4 PIF APF2 interactionfitting models have been calculated successful"
## [1] "24PIF APF2 interactionfitting models have been calculated successful"
## [1] 66
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF EMT_F interactionfitting models have been calculated successful"
## [1] "group2 PIF EMT_F interactionfitting models have been calculated successful"
## [1] "group3 PIF EMT_F interactionfitting models have been calculated successful"
## [1] "group4 PIF EMT_F interactionfitting models have been calculated successful"
## [1] "24PIF EMT_F interactionfitting models have been calculated successful"
## [1] 67
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF FTF1 interactionfitting models have been calculated successful"
## [1] "group2 PIF FTF1 interactionfitting models have been calculated successful"
## [1] "group3 PIF FTF1 interactionfitting models have been calculated successful"
## [1] "group4 PIF FTF1 interactionfitting models have been calculated successful"
## [1] "24PIF FTF1 interactionfitting models have been calculated successful"
## [1] 68
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF FTF2 interactionfitting models have been calculated successful"
## [1] "group2 PIF FTF2 interactionfitting models have been calculated successful"
## [1] "group3 PIF FTF2 interactionfitting models have been calculated successful"
## [1] "group4 PIF FTF2 interactionfitting models have been calculated successful"
## [1] "24PIF FTF2 interactionfitting models have been calculated successful"
## [1] 69
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF MSC_F interactionfitting models have been calculated successful"
## [1] "group2 PIF MSC_F interactionfitting models have been calculated successful"
## [1] "group3 PIF MSC_F interactionfitting models have been calculated successful"
## [1] "group4 PIF MSC_F interactionfitting models have been calculated successful"
## [1] "24PIF MSC_F interactionfitting models have been calculated successful"
## [1] 70
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF MTF interactionfitting models have been calculated successful"
## [1] "group2 PIF MTF interactionfitting models have been calculated successful"
## [1] "group3 PIF MTF interactionfitting models have been calculated successful"
## [1] "group4 PIF MTF interactionfitting models have been calculated successful"
## [1] "24PIF MTF interactionfitting models have been calculated successful"
## [1] 71
## [1] "Cell type interaction in all models calculation"
## [1] "378 Sample were enronlled in the model"
## [1] "group1 PIF MYO_F interactionfitting models have been calculated successful"
## [1] "group2 PIF MYO_F interactionfitting models have been calculated successful"
## [1] "group3 PIF MYO_F interactionfitting models have been calculated successful"
## [1] "group4 PIF MYO_F interactionfitting models have been calculated successful"
## [1] "24PIF MYO_F interactionfitting models have been calculated successful"
## [1] 72
## [1] "All models Selection"
## significant model selected
## [1] 1
## no significant model
## [1] 2
## significant model selected
## [1] 3
## no significant model
## [1] 4
## no significant model
## [1] 5
## no significant model
## [1] 6
## no significant model
## [1] 7
## significant model selected
## [1] 8
## no significant model
## [1] 9
## no significant model
## [1] 10
## significant model selected
## [1] 11
## no significant model
## [1] 12
## no significant model
## [1] 13
## no significant model
## [1] 14
## no significant model
## [1] 15
## no significant model
## [1] 16
## no significant model
## [1] 17
## no significant model
## [1] 18
## significant model selected
## [1] 19
## no significant model
## [1] 20
## no significant model
## [1] 21
## significant model selected
## [1] 22
## no significant model
## [1] 23
## no significant model
## [1] 24
## significant model selected
## [1] 25
## significant model selected
## [1] 26
## significant model selected
## [1] 27
## no significant model
## [1] 28
## no significant model
## [1] 29
## significant model selected
## [1] 30
## no significant model
## [1] 31
## significant model selected
## [1] 32
## no significant model
## [1] 33
## no significant model
## [1] 34
## no significant model
## [1] 35
## no significant model
## [1] 36
## no significant model
## [1] 37
## no significant model
## [1] 38
## no significant model
## [1] 39
## no significant model
## [1] 40
## no significant model
## [1] 41
## no significant model
## [1] 42
## no significant model
## [1] 43
## no significant model
## [1] 44
## no significant model
## [1] 45
## no significant model
## [1] 46
## no significant model
## [1] 47
## no significant model
## [1] 48
## no significant model
## [1] 49
## significant model selected
## [1] 50
## significant model selected
## [1] 51
## no significant model
## [1] 52
## no significant model
## [1] 53
## no significant model
## [1] 54
## no significant model
## [1] 55
## significant model selected
## [1] 56
## no significant model
## [1] 57
## no significant model
## [1] 58
## no significant model
## [1] 59
## significant model selected
## [1] 60
## no significant model
## [1] 61
## no significant model
## [1] 62
## no significant model
## [1] 63
## no significant model
## [1] 64
## significant model selected
## [1] 65
## significant model selected
## [1] 66
## no significant model
## [1] 67
## significant model selected
## [1] 68
## no significant model
## [1] 69
## no significant model
## [1] 70
## significant model selected
## [1] 71
## no significant model
## [1] 72
## [1] "Warning Message: No Adjusted p value in this data"

## IGRAPH 8347389 DNW- 9 72 -- 
## + attr: name (v/c), color (v/c), size (v/n), shape (v/c), label.cex
## | (v/n), label.color (v/c), frame.color (v/c), Pvalue (e/n), OR (e/n),
## | weight (e/n), color (e/c), width (e/n)
## + edges from 8347389 (vertex names):
##  [1] APF2 ->APF1  EMT_F->APF1  FTF1 ->APF1  FTF2 ->APF1  MSC_F->APF1 
##  [6] MTF  ->APF1  MYO_F->APF1  PIF  ->APF1  APF1 ->APF2  EMT_F->APF2 
## [11] FTF1 ->APF2  FTF2 ->APF2  MSC_F->APF2  MTF  ->APF2  MYO_F->APF2 
## [16] PIF  ->APF2  APF1 ->EMT_F APF2 ->EMT_F FTF1 ->EMT_F FTF2 ->EMT_F
## [21] MSC_F->EMT_F MTF  ->EMT_F MYO_F->EMT_F PIF  ->EMT_F APF1 ->FTF1 
## [26] APF2 ->FTF1  EMT_F->FTF1  FTF2 ->FTF1  MSC_F->FTF1  MTF  ->FTF1 
## + ... omitted several edges