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lower the logit threshold to test significance as we observed across …
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…studies that is much sensitive threshold
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@stemangiola
stemangiola committed May 6, 2024
1 parent 364df19 commit f705eb9
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Showing 4 changed files with 11 additions and 11 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -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 = "[email protected]",
role = c("aut", "cre"))
)
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4 changes: 2 additions & 2 deletions R/functions_multi_beta_binomial.R
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Expand Up @@ -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,
Expand Down Expand Up @@ -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,
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4 changes: 2 additions & 2 deletions R/methods.R
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Expand Up @@ -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)
}
Expand All @@ -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){


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12 changes: 6 additions & 6 deletions R/methods_OLD_framework.R
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Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
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