rbbt-dm 1.1.29 → 1.1.30

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 27792718ef802b917873c9eec162237e4d90da2f
-  data.tar.gz: 8fd679e51737d0b95a72b09c2d3802614b9f856b
+  metadata.gz: e20a7775a22a2528277f4f1b6fc70a365ebb7f0f
+  data.tar.gz: 9b421a68b8c47d29e71d0ee502e848b13f617329
 SHA512:
-  metadata.gz: c351b6b4ffdae4cdeeb135ed34690cd4c81eb5de8c4311c0c82e11d5e6100a0354047b9a5b73897c4fd32d77fef93dac31094008e99747a6bf5fb8dd0e0f751b
-  data.tar.gz: 915b6f886c732373161d1b6bc43b51691e692ca50dafa81307890803e435ba4a8ea8de9a6068d13b35028af173da87dbebbdca02aee5a5ce96eede50ebe7dc3f
+  metadata.gz: 2e6683da12ca35ca6e28f3581423d4641c369556b6db34065370856e1db0814deb1e5c747acd4b22c1e032be42809b2d829cb2e52b323fb24adb5616423d04f2
+  data.tar.gz: 49e2fc06719b2838cfbf041f8897abf34adc3451e0201595b7152ecb2afb5b6293fb955067b388324a94c727e77f35deb8a0630e7536a309aeccad66e55472ec

data/lib/rbbt/matrix.rb

@@ -166,7 +166,7 @@ class Matrix
     name = data_file =~ /:>/ ? File.basename(data_file) : data_file
 
     file = Persist.persist(data_file, :tsv, :prefix => "Barcode R #{factor}", :dir => Matrix.matrix_dir.barcode, :no_load => true) do |filename|
-      barcode(filename, factor).to_list
+      barcode(filename, factor)
     end
     subsets = self.subsets
     matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism

data/share/R/barcode.R

@@ -1,5 +1,6 @@
 rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2, key.field = "Ensembl Gene ID"){
-  data = rbbt.tsv(matrix_file)
+  data = rbbt.tsv.numeric(matrix_file)
+
   data.mean = rowMeans(data, na.rm=T)
   data.sd = apply(data, 1, sd, na.rm=T)
   data.threshold = as.matrix(data.mean) + sd.factor * as.matrix(data.sd)
@@ -27,8 +28,7 @@ rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2, key.field =
 }
 
 rbbt.GE.barcode.mode <- function(matrix_file, output_file, sd.factor = 2, key.field = "Ensembl Gene ID"){
-  data = rbbt.tsv(matrix_file)
-  data.mean = rowMeans(data, na.rm=T)
+  data = rbbt.tsv.numeric(matrix_file)
 
   data.mode = apply(data, 1, function(x){ mode = rbbt.get.modes(x)$modes[1]; lower = x[x <= mode]; return(c(lower, mode, lower+mode));})
   data.empty = sapply(data.mode,function(x){ length(x) < 3})
@@ -67,7 +67,8 @@ rbbt.GE.activity_cluster <- function(matrix_file, output_file, key.field = "ID")
 
     library(mclust)
 
-    data = rbbt.tsv(matrix_file)
+    data = rbbt.tsv.numeric(matrix_file)
+
     classes = apply(data,2,function(row){Mclust(row)$classification})
 
     rownames(classes) <- rownames(data)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.29
+  version: 1.1.30
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-10-25 00:00:00.000000000 Z
+date: 2016-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -141,12 +141,12 @@ signing_key:
 specification_version: 4
 summary: Data-mining and statistics
 test_files:
-- test/test_helper.rb
-- test/rbbt/vector/model/test_svm.rb
-- test/rbbt/vector/test_model.rb
 - test/rbbt/network/test_paths.rb
-- test/rbbt/matrix/test_barcode.rb
-- test/rbbt/statistics/test_random_walk.rb
 - test/rbbt/statistics/test_fdr.rb
-- test/rbbt/statistics/test_hypergeometric.rb
+- test/rbbt/statistics/test_random_walk.rb
 - test/rbbt/statistics/test_fisher.rb
+- test/rbbt/statistics/test_hypergeometric.rb
+- test/rbbt/vector/model/test_svm.rb
+- test/rbbt/vector/test_model.rb
+- test/rbbt/matrix/test_barcode.rb
+- test/test_helper.rb