From 56705e0a3b183aab2d1547e95ce4719ab09194a9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 3 Oct 2023 11:05:59 +0200
Subject: [PATCH] switch to poisson clustering

---
 src/bin/kmerclust_boot.R | 4 +---
 src/bin/kmerclust_load.R | 1 -
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/bin/kmerclust_boot.R b/src/bin/kmerclust_boot.R
index 89a7007..eb2e344 100644
--- a/src/bin/kmerclust_boot.R
+++ b/src/bin/kmerclust_boot.R
@@ -5,9 +5,7 @@ load(file = paste0(args[1], ".Rdata"))
 res <- count %>%
   dplyr::select(count_m, count_f) %>%
   as.matrix() %>%
-  compute_tpm() %>%
-  log() %>%
-  compare_models_constraint(count, nboot = as.numeric(args[2]) * 2, bootsize = nrow(count), core = as.numeric(args[2]))
+  poiss_compare_models(count, nboot = as.numeric(args[2]) * 2, bootsize = 1, core = as.numeric(args[2]))
 save(res, file = paste0(args[1], "_boot_", args[3], ".Rdata"))
 
 
diff --git a/src/bin/kmerclust_load.R b/src/bin/kmerclust_load.R
index 235cab9..d8afb0b 100644
--- a/src/bin/kmerclust_load.R
+++ b/src/bin/kmerclust_load.R
@@ -2,7 +2,6 @@ library(kmerclust)
 library(vroom)
 
 args <- commandArgs(trailingOnly = TRUE)
-
 data <- vroom::vroom(args[2], show_col_types = FALSE)
 format(object.size(data), units = "Mb")
 annotation <- parse_annotation(args[1])
-- 
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