rbbt-dm 1.1.23 → 1.1.24
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/matrix.rb +10 -0
- data/lib/rbbt/statistics/rank_product.rb +1 -1
- data/share/R/MA.R +5 -1
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 6d11d8ef4665bf67cfb366e8d4d09cf4c15ab071
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data.tar.gz: 0fcbe23b5740ff83c7f82982720e836628bd0634
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ff7cd428d4e85a6e52f84343932e42dbab7621cd6197d38a0166e90e3bbd791877a436122970d12d884158edccda287e5a34765f96688df1a644d3eb4164fd90
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7
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data.tar.gz: d538ed4a9b3f7b1a6d4b791c52c273a084f7ef697dcbd56d6b7905f8071fa3339a89cb53f99f08c86bc385d168efcd45c06f17b1e76f6d28927d73c836130179
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data/lib/rbbt/matrix.rb
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@@ -147,4 +147,14 @@ class Matrix
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matrix.subsets = subsets
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matrix
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end
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def tsv(to_gene=true, identifiers = nil)
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if to_gene
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file = self.to_gene(identifiers).data_file
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file.tsv :persist => true, :persist_dir => Matrix.matrix_dir.persist, :type => :double, :merge => true, :cast => nil
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else
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self.data_file.tsv :persist => true, :persist_dir => Matrix.matrix_dir.persist, :type => :double, :merge => true, :cast => nil
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end
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end
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end
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@@ -46,7 +46,7 @@ module TSV
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if block_given?
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scores = fields.collect{|field| tsv.sort_by(field, true, &block)}
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else
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scores = fields.collect{|field| tsv.sort_by(field, true){|gene,values|
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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}}
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end
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positions = {}
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data/share/R/MA.R
CHANGED
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@@ -79,6 +79,10 @@ rbbt.dm.matrix.differential <- function(file, main, contrast = NULL, log2 = FALS
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main <- make.names(main);
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contrast <- make.names(contrast);
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data[data == 0] = NA
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good.rows = apply(is.na(data),1,sum) != dim(data)[2]
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data = data[good.rows,]
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ids = rownames(data);
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if (is.null(key.field)){ key.field = "ID" }
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@@ -137,7 +141,7 @@ rbbt.dm.matrix.differential <- function(file, main, contrast = NULL, log2 = FALS
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result = data.frame(ratio = ratio)
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}
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rownames(result) <- original.dimnames[[1]]
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rownames(result) <- original.dimnames[[1]][good.rows]
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if (is.null(outfile)){
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return(result);
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metadata
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-dm
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version: !ruby/object:Gem::Version
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version: 1.1.
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version: 1.1.24
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2016-03-
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date: 2016-03-21 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rbbt-util
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