rbbt-dm 1.1.29 → 1.1.30
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 +1 -1
- data/share/R/barcode.R +5 -4
- metadata +8 -8
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: e20a7775a22a2528277f4f1b6fc70a365ebb7f0f
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data.tar.gz: 9b421a68b8c47d29e71d0ee502e848b13f617329
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 2e6683da12ca35ca6e28f3581423d4641c369556b6db34065370856e1db0814deb1e5c747acd4b22c1e032be42809b2d829cb2e52b323fb24adb5616423d04f2
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7
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data.tar.gz: 49e2fc06719b2838cfbf041f8897abf34adc3451e0201595b7152ecb2afb5b6293fb955067b388324a94c727e77f35deb8a0630e7536a309aeccad66e55472ec
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data/lib/rbbt/matrix.rb
CHANGED
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@@ -166,7 +166,7 @@ class Matrix
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name = data_file =~ /:>/ ? File.basename(data_file) : data_file
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file = Persist.persist(data_file, :tsv, :prefix => "Barcode R #{factor}", :dir => Matrix.matrix_dir.barcode, :no_load => true) do |filename|
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barcode(filename, factor)
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barcode(filename, factor)
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end
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subsets = self.subsets
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matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
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data/share/R/barcode.R
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@@ -1,5 +1,6 @@
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rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2, key.field = "Ensembl Gene ID"){
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data = rbbt.tsv(matrix_file)
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data = rbbt.tsv.numeric(matrix_file)
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data.mean = rowMeans(data, na.rm=T)
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data.sd = apply(data, 1, sd, na.rm=T)
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data.threshold = as.matrix(data.mean) + sd.factor * as.matrix(data.sd)
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@@ -27,8 +28,7 @@ rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2, key.field =
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}
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rbbt.GE.barcode.mode <- function(matrix_file, output_file, sd.factor = 2, key.field = "Ensembl Gene ID"){
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data = rbbt.tsv(matrix_file)
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data.mean = rowMeans(data, na.rm=T)
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data = rbbt.tsv.numeric(matrix_file)
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data.mode = apply(data, 1, function(x){ mode = rbbt.get.modes(x)$modes[1]; lower = x[x <= mode]; return(c(lower, mode, lower+mode));})
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data.empty = sapply(data.mode,function(x){ length(x) < 3})
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@@ -67,7 +67,8 @@ rbbt.GE.activity_cluster <- function(matrix_file, output_file, key.field = "ID")
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library(mclust)
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data = rbbt.tsv(matrix_file)
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data = rbbt.tsv.numeric(matrix_file)
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classes = apply(data,2,function(row){Mclust(row)$classification})
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rownames(classes) <- rownames(data)
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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: 1.1.30
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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-
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date: 2016-12-01 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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@@ -141,12 +141,12 @@ signing_key:
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specification_version: 4
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summary: Data-mining and statistics
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test_files:
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- test/test_helper.rb
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- test/rbbt/vector/model/test_svm.rb
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- test/rbbt/vector/test_model.rb
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- test/rbbt/network/test_paths.rb
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- test/rbbt/matrix/test_barcode.rb
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- test/rbbt/statistics/test_random_walk.rb
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- test/rbbt/statistics/test_fdr.rb
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- test/rbbt/statistics/
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- test/rbbt/statistics/test_random_walk.rb
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- test/rbbt/statistics/test_fisher.rb
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- test/rbbt/statistics/test_hypergeometric.rb
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- test/rbbt/vector/model/test_svm.rb
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- test/rbbt/vector/test_model.rb
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- test/rbbt/matrix/test_barcode.rb
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- test/test_helper.rb
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