424 unique samples | Dorsolateral prefrontal cortex (DLFPC) | ROSMAP cohort

Cytokine families annotation can be found here

Regressions by cell type

Input: Average expression by family.

Numbers and colors : -log10(nominal pvalue)

cutpoints:

< 0.001 = ***

0.01 = **

0.05 = *

0.1 = .

1 = ” ”

Excitatory Neurons

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_ext$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_ext$matrix_pvalue)

Inhibitory Neurons

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_inh$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_inh$matrix_pvalue)

Microglia

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_mic$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_mic$matrix_pvalue)

Oligodendrocytes

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_oli$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_oli$matrix_pvalue)

Astrocytes

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_ast$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_ast$matrix_pvalue)

Oligodendrocyte progenitor cells

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_opc$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_opc$matrix_pvalue)

Endothelial cells

Top results

Top result by covariate.

# res_test$all_stats_df 
createDT(result_end$all_stats_df %>% group_by(phenotype) %>% slice_head(n = 1))

Nominal pvalue

createDT(result_end$matrix_pvalue)

Session info

sessionInfo()
## R version 4.3.2 (2023-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 11 x64 (build 26100)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=Portuguese_Brazil.utf8  LC_CTYPE=Portuguese_Brazil.utf8   
## [3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C                      
## [5] LC_TIME=Portuguese_Brazil.utf8    
## 
## time zone: America/Sao_Paulo
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] performance_0.12.2    lmerTest_3.1-3        lme4_1.1-35.5        
##  [4] Matrix_1.6-5          readxl_1.4.3          RColorBrewer_1.1-3   
##  [7] circlize_0.4.16       ComplexHeatmap_2.18.0 ggsignif_0.6.4       
## [10] ggeasy_0.1.4          ggpubr_0.6.0          lubridate_1.9.3      
## [13] forcats_1.0.0         stringr_1.5.1         purrr_1.0.2          
## [16] tidyr_1.3.1           tibble_3.2.1          tidyverse_2.0.0      
## [19] ggplot2_3.5.0         readr_2.1.5           rstatix_0.7.2        
## [22] dplyr_1.1.4          
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.1    fastmap_1.2.0       digest_0.6.36      
##  [4] timechange_0.3.0    lifecycle_1.0.4     cluster_2.1.4      
##  [7] magrittr_2.0.3      compiler_4.3.2      rlang_1.1.3        
## [10] sass_0.4.9          tools_4.3.2         utf8_1.2.4         
## [13] yaml_2.3.10         knitr_1.48          htmlwidgets_1.6.4  
## [16] plyr_1.8.9          abind_1.4-5         numDeriv_2016.8-1.1
## [19] withr_3.0.1         BiocGenerics_0.48.1 stats4_4.3.2       
## [22] fansi_1.0.6         colorspace_2.1-0    scales_1.3.0       
## [25] iterators_1.0.14    MASS_7.3-60         insight_0.20.3     
## [28] cli_3.6.2           rmarkdown_2.27      crayon_1.5.3       
## [31] generics_0.1.3      rstudioapi_0.16.0   reshape2_1.4.4     
## [34] tzdb_0.4.0          rjson_0.2.21        minqa_1.2.7        
## [37] cachem_1.1.0        splines_4.3.2       parallel_4.3.2     
## [40] cellranger_1.1.0    matrixStats_1.3.0   vctrs_0.6.5        
## [43] boot_1.3-28.1       jsonlite_1.8.8      carData_3.0-5      
## [46] car_3.1-2           IRanges_2.36.0      hms_1.1.3          
## [49] GetoptLong_1.0.5    S4Vectors_0.40.2    clue_0.3-65        
## [52] crosstalk_1.2.1     magick_2.8.4        foreach_1.5.2      
## [55] jquerylib_0.1.4     glue_1.7.0          nloptr_2.1.1       
## [58] codetools_0.2-19    DT_0.33             stringi_1.8.3      
## [61] gtable_0.3.5        shape_1.4.6.1       munsell_0.5.1      
## [64] pillar_1.9.0        htmltools_0.5.8.1   R6_2.5.1           
## [67] doParallel_1.0.17   evaluate_0.24.0     lattice_0.21-9     
## [70] highr_0.11          png_0.1-8           backports_1.4.1    
## [73] broom_1.0.6         bslib_0.8.0         Rcpp_1.0.12        
## [76] nlme_3.1-163        xfun_0.46           pkgconfig_2.0.3    
## [79] GlobalOptions_0.1.2