@@ -18,8 +18,9 @@ of tools for gene expression analysis.

 To install the Bioconductor release version, open R and type:

 ```R

-source("http://bioconductor.org/biocLite.R")

-biocLite("edge")

+if (!requireNamespace("BiocManager", quietly=TRUE))

+    install.packages("BiocManager")

+BiocManager::install("edge")

 ```

 To install the development version, open R and type:

@@ -1,3 +1,4 @@

+<a href="http://www.bioconductor.org/packages/release/bioc/html/edge.html#since"><img border="0" src="http://www.bioconductor.org/shields/years-in-bioc/edge.svg" title="How long since the package was first in a released Bioconductor version (or is it in devel only)."></a> <a href="http://bioconductor.org/packages/stats/bioc/edge.html"><img border="0" src="http://www.bioconductor.org/shields/downloads/edge.svg" title="Percentile (top 5/20/50% or 'available') of downloads over last 6 full months. Comparison is done across all package categories (software, annotation, experiment)."></a> <a href="https://support.bioconductor.org/t/edge/"><img border="0" src="http://www.bioconductor.org/shields/posts/edge.svg" title="Support site activity, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts."></a> <a href="http://www.bioconductor.org/packages/release/bioc/html/edge.html#svn_source"><img border="0" src="http://www.bioconductor.org/shields/commits/bioc/edge.svg" title="average Subversion commits (to the devel branch) per month for the last 6 months"></a>

 edge: Extraction of Differential Gene Expression

 ====

@@ -1,4 +1,4 @@

-edge: Extraction of Differential Expression Analysis

+edge: Extraction of Differential Gene Expression

 ====

 Introduction

@@ -15,12 +15,17 @@ of tools for gene expression analysis.

 ### Installation and Documentation

-To install, open R and type:

+To install the Bioconductor release version, open R and type:

+```R

+source("http://bioconductor.org/biocLite.R")

+biocLite("edge")

+```

+

+To install the development version, open R and type:

 ```R

 install.packages("devtools")

 library("devtools")

-install_github("jdstorey/qvalue", build_vignettes = TRUE)

-install_github("jdstorey/edge", build_vignettes = TRUE)

+install_github(c("jdstorey/qvalue","jdstorey/edge"), build_vignettes = TRUE)

 ```

 Instructions on using edge can be viewed by typing:

@@ -75,7 +80,7 @@ edge_obj <- build_models(data = kidexpr, cov = cov, null.model = null_model, ful

 The `cov` is a data frame of covariates, the `null.model` is the null model and the `full.model` is the alternative model. The input `cov` is a data frame with the column names the same as the variables in the alternative and null models. Once the models have been generated, it is often useful to normalize the gene expression matrix using `apply_snm` and/or adjust for unmodelled variables using `apply_sva`.

 ```R

-edge_norm <- apply_snm(edge_obj)

+edge_norm <- apply_snm(edge_obj, int.var=1:ncol(exprs(edge_obj)), diagnose=FALSE)

 edge_sva <- apply_sva(edge_norm)

 ```

new file mode 100644

@@ -0,0 +1,101 @@

+edge: Extraction of Differential Expression Analysis

+====

+

+Introduction

+------

+The edge package implements methods for carrying out differential

+expression analyses of genome-wide gene expression studies. Significance

+testing using the optimal discovery procedure and generalized likelihood

+ratio tests (equivalent to F-tests and t-tests) are implemented for general study

+designs. Special functions are available to facilitate the analysis of

+common study designs, including time course experiments. Other packages

+such as [snm](http://www.bioconductor.org/packages/release/bioc/html/snm.html), [sva](http://www.bioconductor.org/packages/release/bioc/html/sva.html), and [qvalue](https://github.com/jdstorey/qvalue) are integrated in edge to provide a wide range

+of tools for gene expression analysis.

+

+

+### Installation and Documentation

+

+To install, open R and type:

+```R

+install.packages("devtools")

+library("devtools")

+install_github("jdstorey/qvalue", build_vignettes = TRUE)

+install_github("jdstorey/edge", build_vignettes = TRUE)

+```

+

+Instructions on using edge can be viewed by typing:

+```R

+library("edge")

+browseVignettes("edge")

+```

+

+### Main functions

+* `build_models`

+* `build_study`

+* `odp`

+* `lrt`

+* `fit_models`

+* `kl_clust`

+* `apply_sva`

+* `apply_snm`

+* `apply_qvalue`

+

+### Quick start guide

+

+To get started, first load the kidney dataset included in the package:

+```R

+library(edge)

+data(kidney)

+names(kidney)

+```

+The kidney study is interested in determining differentially expressed genes with respect to age in kidney tissue. The `age` variable is the age of the subjects and the `sex` variable is whether the subjects were male or female. The expression values for the genes are contained in the `kidexpr` variable.

+```R

+kidexpr <- kidney$kidexpr

+age <- kidney$age

+sex <- kidney$sex

+```

+

+Once the data has been loaded, the user has two options to create the experimental models: `build_models` or `build_study`. If the experiment models are unknown to the user, `build_study` can be used to create the models:

+```R

+edge_obj <- build_study(data = kidexpr, adj.var = sex, tme = age, sampling = "timecourse")

+full_model <- fullModel(edge_obj)

+null_model <- nullModel(edge_obj)

+```

+

+The variable `sampling` describes the type of experiment performed, `adj.var` is the adjustment variable and `tme` is the time variable in the study. If the experiment is more complex then type `?build_study` for additional arguments.

+

+If the alternative and null models are known to the user then `build_models` can be used to make a deSet object:

+```R

+library(splines)

+cov <- data.frame(sex = sex, age = age)

+null_model <- ~sex

+full_model <- ~sex + ns(age, df=4)

+edge_obj <- build_models(data = kidexpr, cov = cov, null.model = null_model, full.model = full_model)

+```

+

+The `cov` is a data frame of covariates, the `null.model` is the null model and the `full.model` is the alternative model. The input `cov` is a data frame with the column names the same as the variables in the alternative and null models. Once the models have been generated, it is often useful to normalize the gene expression matrix using `apply_snm` and/or adjust for unmodelled variables using `apply_sva`.

+```R

+edge_norm <- apply_snm(edge_obj)

+edge_sva <- apply_sva(edge_norm)

+

+```

+

+The `odp` or `lrt` function can be used on `edge_sva` to implement either the optimal discovery procedure or the likelihood ratio test, respectively:

+```R

+# optimal discovery procedure

+edge_odp <- odp(edge_sva, bs.its = 30, verbose=FALSE)

+# likelihood ratio test

+edge_lrt <- lrt(edge_sva)

+```

+

+To access the proportional of null p-values estimate, p-values, q-values and local false discovery rates for each gene, use the function `qvalueObj`:

+```R

+qval_obj <- qvalueObj(edge_odp)

+qvals <- qval_obj$qvalues

+pvals <- qval_obj$pvalues

+lfdr <- qval_obj$lfdr

+pi0 <- qval_obj$pi0

+```

+

+See the vignette for more detailed explanations of the edge package.

+