rbbt-dm 1.1.60 → 1.1.62

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: ddc35ddc2c747a98405dd021e4268379f667859d3f62d0bf4785457dc8ab952c
+  metadata.gz: 60fd5ba903985829d71e9253848b9b492542bd596a60916ea4d34fb188d47221
+  data.tar.gz: eca5ce505a41e5fdcc0c8920dd5e4ca0a0cc0415520d24d0d9f6051962154c8b
 SHA512:
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+  data.tar.gz: 9e383e679876331369f76169912d7de34864b569e09e75507e182028156f85762d12ac0d9aaa8f8c39f85d2df01b47f0bdb42597fc4d29ce475db886d3be0223

data/lib/rbbt/matrix.rb

@@ -143,7 +143,7 @@ class RbbtMatrix
   def transpose(id = nil)
     name = data_file =~ /:>/ ? File.basename(data_file) : data_file
 
-    file = Persist.persist(data_file, :tsv, :prefix => "Transpose", :check => [data_file],  :dir => RbbtMatrix.matrix_dir.values, :no_load => true) do
+    file = Persist.persist(data_file, :tsv, :prefix => "Transpose", :check => [data_file], :other => {:id => id},  :dir => RbbtMatrix.matrix_dir.values, :no_load => true) do
 
       data = data_file.tsv(:cast => :to_f, :type => :double).transpose(id)
 

data/share/R/MA.R

@@ -69,7 +69,7 @@ rbbt.dm.matrix.differential.DESeq <- function(expr, subset.main, subset.contrast
     condition_values = rep(c("contrast"), length(subset.contrast))
     condition_values = c(condition_values, rep(c("condition"), length(subset.main)))
     names = c(subset.contrast, subset.main)
-    conditions = data.frame(condition = as.factor(condition_values))
+    conditions = data.frame(condition = factor(condition_values, levels=c("contrast", "condition")))
     
 
     expr = expr[,names]
@@ -79,7 +79,7 @@ rbbt.dm.matrix.differential.DESeq <- function(expr, subset.main, subset.contrast
 
     filter <- HTSFilter(dds, s.len=25, plot=FALSE)$filteredData
 
-    res <- lfcShrink(filter, type="apeglm", coef="condition_contrast_vs_condition")
+    res <- lfcShrink(filter, type="apeglm", coef="condition_condition_vs_contrast")
 
     return(res)
 }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.60
+  version: 1.1.62
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-11-02 00:00:00.000000000 Z
+date: 2022-11-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util