From f705eb9244056c18edb7a59f33f2c80d4a6ce42f Mon Sep 17 00:00:00 2001 From: Stefano Mangiola Date: Mon, 6 May 2024 10:39:49 +1000 Subject: [PATCH] lower the logit threshold to test significance as we observed across studies that is much sensitive threshold --- DESCRIPTION | 2 +- R/functions_multi_beta_binomial.R | 4 ++-- R/methods.R | 4 ++-- R/methods_OLD_framework.R | 12 ++++++------ 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4781fd37..b1362f98 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: sccomp Title: Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data -Version: 1.7.11 +Version: 1.7.12 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com", role = c("aut", "cre")) ) diff --git a/R/functions_multi_beta_binomial.R b/R/functions_multi_beta_binomial.R index 3cfcd00e..77839677 100644 --- a/R/functions_multi_beta_binomial.R +++ b/R/functions_multi_beta_binomial.R @@ -15,7 +15,7 @@ sccomp_glm_data_frame_raw = function(.data, percent_false_positive = 5, check_outliers = TRUE, variational_inference = TRUE, - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, exclude_priors = FALSE, bimodal_mean_variability_association = FALSE, @@ -115,7 +115,7 @@ sccomp_glm_data_frame_counts = function(.data, percent_false_positive = 5, check_outliers = TRUE, variational_inference = TRUE, - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, exclude_priors = FALSE, bimodal_mean_variability_association = FALSE, diff --git a/R/methods.R b/R/methods.R index c37559c8..3fe2c52f 100644 --- a/R/methods.R +++ b/R/methods.R @@ -829,7 +829,7 @@ sccomp_remove_outliers.sccomp_tbl = function(.estimate, sccomp_test <- function(.data, contrasts = NULL, percent_false_positive = 5, - test_composition_above_logit_fold_change = 0.2, + test_composition_above_logit_fold_change = 0.1, pass_fit = TRUE) { UseMethod("sccomp_test", .data) } @@ -844,7 +844,7 @@ sccomp_test <- function(.data, sccomp_test.sccomp_tbl = function(.data, contrasts = NULL, percent_false_positive = 5, - test_composition_above_logit_fold_change = 0.2, + test_composition_above_logit_fold_change = 0.1, pass_fit = TRUE){ diff --git a/R/methods_OLD_framework.R b/R/methods_OLD_framework.R index c6a18710..a595def9 100644 --- a/R/methods_OLD_framework.R +++ b/R/methods_OLD_framework.R @@ -100,7 +100,7 @@ sccomp_glm <- function(.data, cores = detectCores(), percent_false_positive = 5, approximate_posterior_inference = "none", - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, noise_model = "multi_beta_binomial", exclude_priors = FALSE, @@ -130,7 +130,7 @@ sccomp_glm.Seurat = function(.data, cores = detectCores(), percent_false_positive = 5, approximate_posterior_inference = "none", - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, noise_model = "multi_beta_binomial", exclude_priors = FALSE, @@ -192,7 +192,7 @@ sccomp_glm.SingleCellExperiment = function(.data, cores = detectCores(), percent_false_positive = 5, approximate_posterior_inference = "none", - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, noise_model = "multi_beta_binomial", exclude_priors = FALSE, @@ -257,7 +257,7 @@ sccomp_glm.DFrame = function(.data, cores = detectCores(), percent_false_positive = 5, approximate_posterior_inference = "none", - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, noise_model = "multi_beta_binomial", exclude_priors = FALSE, @@ -320,7 +320,7 @@ sccomp_glm.data.frame = function(.data, cores = detectCores(), percent_false_positive = 5, approximate_posterior_inference = "none", - test_composition_above_logit_fold_change = 0.2, .sample_cell_group_pairs_to_exclude = NULL, + test_composition_above_logit_fold_change = 0.1, .sample_cell_group_pairs_to_exclude = NULL, verbose = FALSE, noise_model = "multi_beta_binomial", exclude_priors = FALSE, @@ -462,7 +462,7 @@ sccomp_glm.data.frame = function(.data, test_contrasts <- function(.data, contrasts = NULL, percent_false_positive = 5, - test_composition_above_logit_fold_change = 0.2, + test_composition_above_logit_fold_change = 0.1, pass_fit = TRUE) { # DEPRECATE