rbbt-dm 1.1.23 → 1.1.24

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e243ce5032fd1fecaa9cec716678f8882c50a54e
-  data.tar.gz: d2b58265604a3933eb4b6528cbb57faf424c9aea
+  metadata.gz: 6d11d8ef4665bf67cfb366e8d4d09cf4c15ab071
+  data.tar.gz: 0fcbe23b5740ff83c7f82982720e836628bd0634
 SHA512:
-  metadata.gz: 450a0de2320972c6848b1d88af2faf11743c48fdf0c5013232df25d7bb1686487cae7e1cd97c7ceb9863d7e7b66d2e969b9b27631569efde3aa78d6bb68dc69a
-  data.tar.gz: 215e2140ba429f94d1dd452c867e4ce611efa520c309a2c5003a45ea9dc463bf55d8f0272ce8111c6dc518519d539b78653eecb6680cf94df3b6b5eae5599aaa
+  metadata.gz: ff7cd428d4e85a6e52f84343932e42dbab7621cd6197d38a0166e90e3bbd791877a436122970d12d884158edccda287e5a34765f96688df1a644d3eb4164fd90
+  data.tar.gz: d538ed4a9b3f7b1a6d4b791c52c273a084f7ef697dcbd56d6b7905f8071fa3339a89cb53f99f08c86bc385d168efcd45c06f17b1e76f6d28927d73c836130179

data/lib/rbbt/matrix.rb

@@ -147,4 +147,14 @@ class Matrix
     matrix.subsets = subsets
     matrix
   end
+
+  def tsv(to_gene=true, identifiers = nil)
+    if to_gene
+      file =  self.to_gene(identifiers).data_file
+      file.tsv :persist => true, :persist_dir => Matrix.matrix_dir.persist, :type => :double, :merge => true, :cast => nil
+    else
+      self.data_file.tsv :persist => true, :persist_dir => Matrix.matrix_dir.persist, :type => :double, :merge => true, :cast => nil
+    end
+  end
+
 end

data/lib/rbbt/statistics/rank_product.rb

@@ -46,7 +46,7 @@ module TSV
     if block_given?
       scores = fields.collect{|field| tsv.sort_by(field, true, &block)}
     else
-      scores = fields.collect{|field| tsv.sort_by(field, true){|gene,values| tsv.type == :single ? values.to_f : values.flatten.first.to_f}}
+      scores = fields.collect{|field| tsv.sort_by(field, true){|gene,values|  (tsv.type == :single or tsv.type == :list) ? values.to_f : values.flatten.first.to_f}}
     end
     positions = {}
     

data/share/R/MA.R

@@ -79,6 +79,10 @@ rbbt.dm.matrix.differential <- function(file, main, contrast = NULL, log2 = FALS
     main <- make.names(main);
     contrast <- make.names(contrast);
 
+    data[data == 0] = NA
+    good.rows = apply(is.na(data),1,sum) != dim(data)[2]
+    data = data[good.rows,]
+
     ids = rownames(data);
     if (is.null(key.field)){ key.field = "ID" }
 
@@ -137,7 +141,7 @@ rbbt.dm.matrix.differential <- function(file, main, contrast = NULL, log2 = FALS
        result = data.frame(ratio = ratio)
     }
 
-    rownames(result) <- original.dimnames[[1]]
+    rownames(result) <- original.dimnames[[1]][good.rows]
 
    if (is.null(outfile)){
        return(result);

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.23
+  version: 1.1.24
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-14 00:00:00.000000000 Z
+date: 2016-03-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util