diff --git a/.DS_Store b/.DS_Store index f5abc87..40a385f 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/.Rbuildignore b/.Rbuildignore index 168b747..a68349c 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,6 +8,10 @@ #For the cached chunks of README.Rmd ^cache*$ ^README_cache*$ +#For the cached chunks of the vignettes +^vignettes.*cache$ +#For the image outputs of the vignettes +^vignettes.*files$ #If README too big, not on CRAN but only on git ^man/figures*$ ^README\.Rmd$ diff --git a/Patterns.Rproj b/Patterns.Rproj index fe9f167..bdc2d83 100755 --- a/Patterns.Rproj +++ b/Patterns.Rproj @@ -15,7 +15,6 @@ LaTeX: pdfLaTeX BuildType: Package PackageUseDevtools: Yes PackageInstallArgs: --no-multiarch --with-keep.source -PackageBuildBinaryArgs: --no-build-vignettes PackageCheckArgs: --as-cran QuitChildProcessesOnExit: Yes diff --git a/README.Rmd b/README.Rmd index cbfda31..ababaff 100644 --- a/README.Rmd +++ b/README.Rmd @@ -28,15 +28,17 @@ It allows for **single** or **joint modeling** of, for instance, genes and prote * It starts with the **selection of the actors** that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its **differential effects** (for instance gene expression or protein abundance) or on its **time course profile**. * Wrappers for **actors clustering** functions and cluster analysis are provided. -* It also allows **reverse engineering** of biological networks taking into account the observed time course patterns of the actors. Many **inference functions** are provided with the `Patterns` package and dedicated to get **specific features** for the inferred network such as **sparsity**, **robust links**, **high confidence links** or **stable through resampling links**. - + **LASSO**, from the `lars` package - + **LASSO2**, from the `glmnet` package. An unweighted and a weighted version of the algorithm are available - + **SPLS**, from the `spls` package - + **ELASTICNET**, from the `elasticnet` package - + **stability.c060**, from the `c060` package implementation of stability selection - + **stability.c060.weighted**, a new weighted version of the `c060` package implementation of stability selection +* It also allows **reverse engineering** of biological networks taking into account the observed time course patterns of the actors. Interactions between clusters of actors can be set by the user. Any number of clusters can be activated at a single time. +* Many **inference functions** are provided with the `Patterns` package and dedicated to get **specific features** for the inferred network such as **sparsity**, **robust links**, **high confidence links** or **stable through resampling links**. + + **lasso**, from the `lars` package + + **lasso**, from the `glmnet` package. An unweighted and a weighted version of the algorithm are available + + **spls**, from the `spls` package + + **elasticnet**, from the `elasticnet` package + + **stability selection**, from the `c060` package implementation of stability selection + + **weighted stability selection**, a new weighted version of the `c060` package implementation of stability selection that I created for the package + **robust**, lasso from the `lars` package with light random Gaussian noise added to the explanatory variables - + **selectboost.weighted**, a new weighted version of the `selectboost` package implementation of the selectboost algorithm to look for the more stable links against resampling that takes into account the correlated structure of the predictors. If no weights are provided, equal weigths are for all the variables (=non weighted case). + + **selectboost**, from the `selectboost` package. The selectboost algorithm looks for the more stable links against resampling that takes into account the correlated structure of the predictors + + **weighted selectboost**, a new weighted version of the `selectboost`. * Some **simulation** and **prediction** tools are also available for cascade networks. * Examples of use with microarray or RNA-Seq data are provided. diff --git a/README.md b/README.md index 302e0c9..4613e35 100644 --- a/README.md +++ b/README.md @@ -19,15 +19,17 @@ It allows for **single** or **joint modeling** of, for instance, genes and prote * It starts with the **selection of the actors** that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its **differential effects** (for instance gene expression or protein abundance) or on its **time course profile**. * Wrappers for **actors clustering** functions and cluster analysis are provided. -* It also allows **reverse engineering** of biological networks taking into account the observed time course patterns of the actors. Many **inference functions** are provided with the `Patterns` package and dedicated to get **specific features** for the inferred network such as **sparsity**, **robust links**, **high confidence links** or **stable through resampling links**. - + **LASSO**, from the `lars` package - + **LASSO2**, from the `glmnet` package. An unweighted and a weighted version of the algorithm are available - + **SPLS**, from the `spls` package - + **ELASTICNET**, from the `elasticnet` package - + **stability.c060**, from the `c060` package implementation of stability selection - + **stability.c060.weighted**, a new weighted version of the `c060` package implementation of stability selection +* It also allows **reverse engineering** of biological networks taking into account the observed time course patterns of the actors. Interactions between clusters of actors can be set by the user. Any number of clusters can be activated at a single time. +* Many **inference functions** are provided with the `Patterns` package and dedicated to get **specific features** for the inferred network such as **sparsity**, **robust links**, **high confidence links** or **stable through resampling links**. + + **lasso**, from the `lars` package + + **lasso**, from the `glmnet` package. An unweighted and a weighted version of the algorithm are available + + **spls**, from the `spls` package + + **elasticnet**, from the `elasticnet` package + + **stability selection**, from the `c060` package implementation of stability selection + + **weighted stability selection**, a new weighted version of the `c060` package implementation of stability selection that I created for the package + **robust**, lasso from the `lars` package with light random Gaussian noise added to the explanatory variables - + **selectboost.weighted**, a new weighted version of the `selectboost` package implementation of the selectboost algorithm to look for the more stable links against resampling that takes into account the correlated structure of the predictors. If no weights are provided, equal weigths are for all the variables (=non weighted case). + + **selectboost**, from the `selectboost` package. The selectboost algorithm looks for the more stable links against resampling that takes into account the correlated structure of the predictors + + **weighted selectboost**, a new weighted version of the `selectboost`. * Some **simulation** and **prediction** tools are also available for cascade networks. * Examples of use with microarray or RNA-Seq data are provided. diff --git a/docs/articles/Patterns.html b/docs/articles/IntroPatterns.html similarity index 54% rename from docs/articles/Patterns.html rename to docs/articles/IntroPatterns.html index 69bc3ff..f457ac4 100644 --- a/docs/articles/Patterns.html +++ b/docs/articles/IntroPatterns.html @@ -42,9 +42,6 @@ -
  • - Get started -
  • Reference
  • @@ -58,6 +55,9 @@
  • Network inference and analysis of CLL data
  • +
  • + Patterns: a modeling tool dedicated to biological network modeling +
  • @@ -91,8 +91,8 @@

    Frédéric Bertrand

    2019-05-03

    - Source: vignettes/Patterns.Rmd - + Source: vignettes/IntroPatterns.Rmd + @@ -105,24 +105,27 @@

    The weights are viewed as a penalty factors in the penalized regression model: it is a number that multiplies the lambda value in the minimization problem to allow differential shrinkage, Friedman et al. 2010, equation 1 page 3. If equal to 0, it implies no shrinkage, and that variable is always included in the model. Default is 1 for all variables. Infinity means that the variable is excluded from the model. Note that the weights are rescaled to sum to the number of variables.

    Due to maximum size requirement for CRAN packages, most of the graphics of the vignette will be created when the code is run.

    - - - - - - - - + + + + + + + +

    A word for those that have been using our seminal work, the Cascade package that we created several years ago and that was a very efficient network reverse engineering tool for cascade networks (Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014), https://doi.org/10.1093/bioinformatics/btt705, https://cran.r-project.org/package=Cascade, https://github.com/fbertran/Cascade and https://fbertran.github.io/Cascade/).

    The Patterns package is more than (at least) a threeway major extension of the Cascade package :

  • @@ -123,7 +123,7 @@

    All vignettes

    diff --git a/docs/authors.html b/docs/authors.html index 2bfdcf7..d2fd627 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -72,9 +72,6 @@
  • -
  • - Get started -
  • Reference
  • @@ -88,6 +85,9 @@
  • Network inference and analysis of CLL data
  • +
  • + Patterns: a modeling tool dedicated to biological network modeling +
  • diff --git a/docs/index.html b/docs/index.html index 2b4ecd8..c7c8e72 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,9 +42,6 @@
  • -
  • - Get started -
  • Reference
  • @@ -58,6 +55,9 @@
  • Network inference and analysis of CLL data
  • +
  • + Patterns: a modeling tool dedicated to biological network modeling +
  • @@ -95,24 +95,27 @@
  • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 39aeded..b20a9fa 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 1.3.0 pkgdown_sha: ~ articles: ExampleCLL: ExampleCLL.html - Patterns: Patterns.html + IntroPatterns: IntroPatterns.html diff --git a/docs/reference/index.html b/docs/reference/index.html index 7ad85fc..8c41101 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -72,9 +72,6 @@
  • -
  • - Get started -
  • Reference
  • @@ -88,6 +85,9 @@
  • Network inference and analysis of CLL data
  • +
  • + Patterns: a modeling tool dedicated to biological network modeling +
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index 542a857..69790eb 100644 Binary files a/vignettes/ExampleCLL_files/figure-html/plotTFinsel2-1.png and b/vignettes/ExampleCLL_files/figure-html/plotTFinsel2-1.png differ diff --git a/vignettes/Patterns.Rmd b/vignettes/IntroPatterns.Rmd similarity index 91% rename from vignettes/Patterns.Rmd rename to vignettes/IntroPatterns.Rmd index 64f6a68..33e6070 100644 --- a/vignettes/Patterns.Rmd +++ b/vignettes/IntroPatterns.Rmd @@ -33,15 +33,17 @@ It allows for **single** or **joint modeling** of, for instance, genes and prote * It starts with the **selection of the actors** that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its **differential effects** (for instance gene expression or protein abundance) or on its **time course profile**. * Wrappers for **actors clustering** functions and cluster analysis are provided. -* It also allows **reverse engineering** of biological networks taking into account the observed time course patterns of the actors. Many **inference functions** are provided with the `Patterns` package and dedicated to get **specific features** for the inferred network such as **sparsity**, **robust links**, **high confidence links** or **stable through resampling links**. - + **LASSO**, from the `lars` package - + **LASSO2**, from the `glmnet` package. An unweighted and a weighted version of the algorithm are available - + **SPLS**, from the `spls` package - + **ELASTICNET**, from the `elasticnet` package - + **stability.c060**, from the `c060` package implementation of stability selection - + **stability.c060.weighted**, a new weighted version of the `c060` package implementation of stability selection +* It also allows **reverse engineering** of biological networks taking into account the observed time course patterns of the actors. Interactions between clusters of actors can be set by the user. Any number of clusters can be activated at a single time. +* Many **inference functions** are provided with the `Patterns` package and dedicated to get **specific features** for the inferred network such as **sparsity**, **robust links**, **high confidence links** or **stable through resampling links**. + + **lasso**, from the `lars` package + + **lasso**, from the `glmnet` package. An unweighted and a weighted version of the algorithm are available + + **spls**, from the `spls` package + + **elasticnet**, from the `elasticnet` package + + **stability selection**, from the `c060` package implementation of stability selection + + **weighted stability selection**, a new weighted version of the `c060` package implementation of stability selection that I created for the package + **robust**, lasso from the `lars` package with light random Gaussian noise added to the explanatory variables - + **selectboost.weighted**, a new weighted version of the `selectboost` package implementation of the selectboost algorithm to look for the more stable links against resampling that takes into account the correlated structure of the predictors. If no weights are provided, equal weigths are for all the variables (=non weighted case). + + **selectboost**, from the `selectboost` package. The selectboost algorithm looks for the more stable links against resampling that takes into account the correlated structure of the predictors + + **weighted selectboost**, a new weighted version of the `selectboost`. * Some **simulation** and **prediction** tools are also available for cascade networks. * Examples of use with microarray or RNA-Seq data are provided. @@ -51,35 +53,35 @@ The weights are viewed as a penalty factors in the penalized regression model: i Due to maximum size requirement for CRAN packages, most of the graphics of the vignette will be created when the code is run. - + - + - + - + - + - + - + - + A word for those that have been using our seminal work, the `Cascade` package that we created several years ago and that was a very efficient network reverse engineering tool for cascade networks @@ -497,7 +499,7 @@ evolution(network,sequence,type.ani = "html") ``` Evolution of some properties of a reverse-engineered network with increasing cut-off values. -![Evolution of some properties of a reverse-engineered network with increasing cut-off values.](Patterns_files/compare-methods-1.png) +![Evolution of some properties of a reverse-engineered network with increasing cut-off values.](IntroPatterns_files/compare-methods-1.png) We switch to data that were derived from the inferrence of a real biological network and try to detect the optimal cutoff value: the best cutoff value for a network to fit a scale free network. The `cutoff` was validated only single group cascade networks (number of actors groups = number of timepoints) and for genes dataset. 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