The goal of scACCorDiON.su is to run survival analysis on the results of scACCorDiON.
You can install the development version of scACCorDiON.su like so:
pak::pak("CostaLab/scACCorDiON.su")This is a basic example of how you could run this pipeline:
library(scACCorDiON.su)
#> ---------------------------------
#> scACCorDiON.su version 0.0.0.9000
#> ---------------------------------
data(pdac_cci_data)
data(paad_tcga_clinical_data)
data(paad_tcga_expression_data)
data(comparison_of_interest)
results <-
run_survival(
comparison_oi = comparison_of_interest,
lr_data = pdac_cci_data,
tcga_exp_data = paad_tcga_expression_data,
tcga_clinical_data = paad_tcga_clinical_data,
selection_method = c("limma"),
custom_selection = NULL,
n_lr_selected = 5,
which_get = c("ligand", "receptor"),
is_signif = TRUE,
clinical_vars_in_model = c("stage")
)
#> Warning: Zero sample variances detected, have been offset away from zero
results$cox_models$coxph_clinical.lr_pairs |>
broom::tidy() |>
print()
#> # A tibble: 8 × 5
#> term estimate std.error statistic p.value
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 stageStage_II 0.244 0.430 0.567 0.571
#> 2 stageStage_III -0.497 1.09 -0.458 0.647
#> 3 stageStage_IV 0.194 0.832 0.234 0.815
#> 4 PCSK9_VLDLR 0.139 0.102 1.36 0.172
#> 5 TNFSF11_TNFRSF11A 0.0823 0.123 0.668 0.504
#> 6 WNT7B_FZD1 0.154 0.129 1.19 0.233
#> 7 DKK1_KREMEN1 0.191 0.118 1.62 0.105
#> 8 L1CAM_EPHB2 0.0170 0.104 0.163 0.871