Linear/Logistic Regression

Read data and prepare inputs

Prepare parameters

covariates = c("age_death","msex", "educ", "pmi")

pheno_list = c(
  "apoe_any4"="binomial"
)

Run association tests

assoc_results = list()
for(cell_i in names(celltype_exp)) {
  exprData = as.data.frame(celltype_exp[[cell_i]])
  
  # Filter the gene expression
  exprData_ensembl = gsub("(.*)\\.(.*)","\\1", rownames(exprData)) 
  exprData_filt = exprData[exprData_ensembl %in% cytokines$ensembl, ]
  exprData_filt$ensembl = gsub("(.*)\\.(.*)","\\1",rownames(exprData_filt))
  exprData_cytokines = merge(exprData_filt, cytokines, by = "ensembl")
  rownames(exprData_cytokines) = exprData_cytokines$symbol
  exprData_cytokines$ensembl = NULL
  exprData_cytokines$symbol = NULL
  
  data4linear_reg <- as.data.frame(t(exprData_cytokines))
  phenotype_dt <- pheno_SN[match(rownames(data4linear_reg), pheno_SN$projid), ]
  
  res_test = run_module_trait_association(data4linear_reg, 
                                          phenotype_dt, 
                                          pheno_list,
                                          covariates = covariates)
  
  assoc_results[[cell_i]] = res_test
}

## Loading required package: lme4

## Loading required package: Matrix

## 
## Attaching package: 'Matrix'

## The following objects are masked from 'package:tidyr':
## 
##     expand, pack, unpack

## Loading required package: lmerTest

## 
## Attaching package: 'lmerTest'

## The following object is masked from 'package:lme4':
## 
##     lmer

## The following object is masked from 'package:stats':
## 
##     step

## Loading required package: performance

## Loading required package: ggeffects

## Loading required package: parameters

## Loading required package: datawizard

## 
## Attaching package: 'datawizard'

## The following objects are masked from 'package:ggpubr':
## 
##     mean_sd, median_mad

## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(HGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(THPO) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL7) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C5) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(VEGFA) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF4) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(PSPN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF9) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(EGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL14) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL18) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CCL28) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL34) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL15) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL16) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL17D) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL17) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(DCN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IGF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(HGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL7) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C5) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(VEGFA) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF4) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(PSPN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF9) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C3) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(EGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL14) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL18) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL34) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL15) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL16) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL17D) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(NOG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(DCN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IGF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(HGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL7) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C5) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(VEGFA) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF4) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(PSPN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF9) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C3) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL14) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL18) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL34) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(GDNF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL17D) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CSF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IFNA2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL17) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IFNA13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(DCN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(HGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FLT3LG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL7) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C5) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(VEGFA) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF4) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(PSPN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C3) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL33) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(EGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL14) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CTF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL18) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL34) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL15) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL17D) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CSF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL17) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FLT3LG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL7) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C5) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(VEGFA) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL14) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL18) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL34) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(GDNF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL17D) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CSF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL17) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IGF1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(HGF) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FLT3LG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL7) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(EBI3) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C5) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF8) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(VEGFA) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL1A) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF10) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL1B) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(C3) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CXCL14) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL18) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL34) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF13) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL15) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL16) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL17D) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(CX3CL1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL32) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(DCN) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(KITLG) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TGFB1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(SPP1) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF10) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(FGF2) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(IL15) +  age_death + msex + educ + pmi"
## [1] "Testing (n=423): scale(apoe_any4) ~ scale(TNFSF12) +  age_death + msex + educ + pmi"

save(assoc_results, file = file.path(work_dir, "cytokines_snRNA_APOE_association_results.RData"))

all_stats = lapply(assoc_results, function(x) x$all_stats_df) %>% 
  bind_rows(.id = "cell_type") %>% 
  mutate(cell_type = factor(cell_type, levels = names(celltype_exp))) %>%
  arrange(p)

ext

createDT(all_stats[all_stats$cell_type == "ext",])

inh

createDT(all_stats[all_stats$cell_type == "inh",])

oli

createDT(all_stats[all_stats$cell_type == "oli",])

ast

createDT(all_stats[all_stats$cell_type == "ast",])

opc

createDT(all_stats[all_stats$cell_type == "opc",])

mic

createDT(all_stats[all_stats$cell_type == "mic",])

end

createDT(all_stats[all_stats$cell_type == "end",])

Session info

sessionInfo()

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Stream 8
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] datawizard_0.13.0     parameters_0.22.1     ggeffects_1.7.2      
##  [4] performance_0.12.2    lmerTest_3.1-3        lme4_1.1-35.1        
##  [7] Matrix_1.6-5          RColorBrewer_1.1-3    circlize_0.4.16      
## [10] ComplexHeatmap_2.15.4 ggsignif_0.6.4        data.table_1.17.6    
## [13] ggeasy_0.1.5          ggpubr_0.6.0          lubridate_1.9.3      
## [16] forcats_1.0.0         stringr_1.5.1         purrr_1.0.4          
## [19] tidyr_1.3.1           tibble_3.3.0          tidyverse_2.0.0      
## [22] ggplot2_3.5.1         readr_2.1.5           rstatix_0.7.2        
## [25] dplyr_1.1.4          
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-153        matrixStats_1.5.0   bit64_4.6.0-1      
##  [4] insight_0.20.5      doParallel_1.0.17   numDeriv_2016.8-1.1
##  [7] tools_4.1.2         backports_1.5.0     bslib_0.8.0        
## [10] DT_0.33             R6_2.6.1            BiocGenerics_0.40.0
## [13] colorspace_2.1-1    GetoptLong_1.0.5    withr_3.0.2        
## [16] tidyselect_1.2.1    emmeans_1.10.5      bit_4.6.0          
## [19] compiler_4.1.2      cli_3.6.5           sandwich_3.1-1     
## [22] bayestestR_0.15.0   sass_0.4.9          scales_1.3.0       
## [25] mvtnorm_1.3-2       digest_0.6.37       minqa_1.2.8        
## [28] rmarkdown_2.29      pkgconfig_2.0.3     htmltools_0.5.8.1  
## [31] fastmap_1.2.0       htmlwidgets_1.6.4   rlang_1.1.6        
## [34] GlobalOptions_0.1.2 rstudioapi_0.17.1   shape_1.4.6.1      
## [37] jquerylib_0.1.4     generics_0.1.4      zoo_1.8-12         
## [40] jsonlite_2.0.0      crosstalk_1.2.1     vroom_1.6.5        
## [43] car_3.1-3           magrittr_2.0.3      Formula_1.2-5      
## [46] Rcpp_1.0.14         munsell_0.5.1       S4Vectors_0.32.4   
## [49] abind_1.4-8         lifecycle_1.0.4     multcomp_1.4-26    
## [52] stringi_1.8.7       yaml_2.3.10         carData_3.0-5      
## [55] MASS_7.3-60.0.1     parallel_4.1.2      crayon_1.5.3       
## [58] lattice_0.20-45     splines_4.1.2       hms_1.1.3          
## [61] knitr_1.49          pillar_1.10.2       boot_1.3-28        
## [64] rjson_0.2.23        estimability_1.5.1  codetools_0.2-18   
## [67] stats4_4.1.2        glue_1.8.0          evaluate_1.0.1     
## [70] png_0.1-8           vctrs_0.6.5         nloptr_2.1.1       
## [73] tzdb_0.4.0          foreach_1.5.2       gtable_0.3.6       
## [76] clue_0.3-66         cachem_1.1.0        xfun_0.49          
## [79] xtable_1.8-4        broom_1.0.7         coda_0.19-4.1      
## [82] survival_3.7-0      iterators_1.0.14    IRanges_2.28.0     
## [85] cluster_2.1.2       timechange_0.3.0    TH.data_1.1-2

Associations - APOE - snRNA-seq

Ricardo A. Vialle, Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
Juliana Beker Godoy, MSc - Graduate program in Bioinformatics, UFPR, Curitiba, Brazil
Katia de Paiva Lopes, Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA

2025-08-01

Linear/Logistic Regression

Read data and prepare inputs

Prepare parameters

Run association tests

ext

inh

oli

ast

opc

mic

end

Session info

Associations - APOE - snRNA-seq

Ricardo A. Vialle, Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA Juliana Beker Godoy, MSc - Graduate program in Bioinformatics, UFPR, Curitiba, Brazil Katia de Paiva Lopes, Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA

2025-08-01

Linear/Logistic Regression

Read data and prepare inputs

Prepare parameters

Run association tests

ext

inh

oli

ast

opc

mic

end

Session info

Ricardo A. Vialle, Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
Juliana Beker Godoy, MSc - Graduate program in Bioinformatics, UFPR, Curitiba, Brazil
Katia de Paiva Lopes, Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA