version 1.0.12

cran · Jun 27, 2024 · 226d005 · 226d005
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DEET
 Title: Differential Expression Enrichment Tool
-Version: 1.0.11
+Version: 1.0.12
 Authors@R: 
   c(person(given = "Dustin",
            family = "Sokolowski",
@@ -40,7 +40,7 @@ URL:
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
-Packaged: 2023-08-17 03:26:16 UTC; djsok
+Packaged: 2024-06-26 03:56:49 UTC; djsok
 Suggests: testthat, knitr, rmarkdown
 VignetteBuilder: knitr
 NeedsCompilation: no
@@ -52,4 +52,4 @@ Author: Dustin Sokolowski [aut, cre],
   Anna Goldenberg [aut],
   Michael Wilson [aut]
 Repository: CRAN
-Date/Publication: 2023-08-17 07:52:51 UTC
+Date/Publication: 2024-06-26 10:50:02 UTC
diff --git a/MD5 b/MD5
@@ -1,7 +1,7 @@
-ab6a9ef574acc1739fd6fcf1f94b43e4 *DESCRIPTION
+9b087c5f36a2ae2c0c4f519a3fcda855 *DESCRIPTION
 a6802c7b81513b1f3845b5ccfdd85238 *NAMESPACE
 57784e13a41ad885455a938ffcce17ec *R/DEET_Input_as_Reference.R
-a4da34544409e9a172d195d63e10f0b4 *R/DEET_data_download.R
+9d9efb4d3a6d2600ed3f4fb4da15a047 *R/DEET_data_download.R
 e014f82255db849211c3503b9669fbaa *R/DEET_enrich.R
 16e255bdf01d3c19c799a8251a4007cf *R/DEET_enrich_genesonly.R
 c4040ac47140545880a8dfd73e8576f2 *R/DEET_enrichment_plot.R
@@ -20,8 +20,8 @@ c64a037b89e694d8d48a9d7e218b0378 *data/DEET_example_data.rda
 982fb7b7aec2fad60d30395f3878f26d *data/DEET_feature_extract_example_response.rda
 91d8f778fe689a3f9c00130e96ce0aed *data/example_DEET_enrich_input.rda
 e35c34bae88c1674949e04202ef83231 *inst/doc/DEET_vignette.R
-0ff0dee399e307ca8cc9c78aa3065c99 *inst/doc/DEET_vignette.Rmd
-f46f728385a6992ddded7ec42866f91f *inst/doc/DEET_vignette.html
+cfdab8c7452d0d73f2fb8388ddb57f7c *inst/doc/DEET_vignette.Rmd
+04bcdace4fecec351d6962979202200f *inst/doc/DEET_vignette.html
 deb760d6b80e24b0b3e652603cf82d4e *man/DEET_Input_as_Reference.Rd
 7018d03cfff557b0fdc4ac3724327b36 *man/DEET_data_download.Rd
 abc1a23a22a1aa67cc372c838aef5903 *man/DEET_enrich.Rd
@@ -39,4 +39,4 @@ d2c0ccf97380224ae74e46398d4af58a *tests/testthat.R
 9ef93134ab287dc725089268cdc4a0f2 *tests/testthat/test_DEET_enrich.R
 558d9c00f9878c4f05aa9ffd24e30a11 *tests/testthat/test_DEET_feature_extract.R
 9c9944324287f204e9b86d11e7a8e591 *vignettes/DEET_V2.png
-0ff0dee399e307ca8cc9c78aa3065c99 *vignettes/DEET_vignette.Rmd
+cfdab8c7452d0d73f2fb8388ddb57f7c *vignettes/DEET_vignette.Rmd
diff --git a/R/DEET_data_download.R b/R/DEET_data_download.R
@@ -82,7 +82,7 @@ DEET_data_download <- function(x = "enrich") {
     if(i %in% "metadata") {
       datafile <- "DEET_metadata.rda"
       metafile <- paste0(datafile)
-      url <- paste0("http://wilsonlab.org/public/DEET_data/",
+      url <- paste0("http://www.wilsonlab.org/public/DEET_data/",
                     metafile, "?raw=true")
       destfile <- file.path(tempdir(), metafile)
       downloader::download(url, destfile = destfile, mode = "wb")
@@ -92,7 +92,7 @@ DEET_data_download <- function(x = "enrich") {
     if(i %in% "enrich") {
       datafile <- "DEET_combined.rda"
       metafile <- paste0(datafile)
-      url <- paste0("http://wilsonlab.org/public/DEET_data/",
+      url <- paste0("http://www.wilsonlab.org/public/DEET_data/",
                     metafile, "?raw=true")
       destfile <- file.path(tempdir(), metafile)
       downloader::download(url, destfile = destfile, mode = "wb")
@@ -102,7 +102,7 @@ DEET_data_download <- function(x = "enrich") {
     if(i %in% "feature_matrix") {
       datafile <- "DEET_log2FC_matrix.rda"
       metafile <- paste0(datafile)
-      url <- paste0("http://wilsonlab.org/public/DEET_data/",
+      url <- paste0("http://www.wilsonlab.org/public/DEET_data/",
                     metafile, "?raw=true")
       destfile <- file.path(tempdir(), metafile)
       downloader::download(url, destfile = destfile, mode = "wb")

diff --git a/inst/doc/DEET_vignette.Rmd b/inst/doc/DEET_vignette.Rmd
@@ -48,7 +48,7 @@ devtools::install_github("wilsonlabgroup/DEET")
 
 ## Downloading files
 
-All processed DEGs, metadata, and enriched pathways in formats compatible with this package as well as other methods such as gene set enrichment analysis are stored here: http://wilsonlab.org/public/DEET_data/
+All processed DEGs, metadata, and enriched pathways in formats compatible with this package as well as other methods such as gene set enrichment analysis are stored here: https://www.wilsonlab.org/public/DEET_data/
 
 No functions within DEET automatically load data for the user, so the data either needs to be downloaded directly from the ftp, or using the downloader function.
 
@@ -87,8 +87,8 @@ This is the meat and potatoes of the DEET dataset. Here, you can find all of the
 * DEET_gmt_BP: A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the pathways that are enriched within that study.
 * DEET_gmt_TF: A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the TFs that are enriched within that study.
 * DEET_gmt_DE: A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the DEGs that are enriched within that study.
-* gmt_BP: A list of class GMT, which is a curated human gene ontology  gene sets from the Bader Lab `http://download.baderlab.org/EM_Genesets/`. 
-* gmt_TF: A list of class GMT, which is a curated human transcription factor gene sets from the Bader Lab `http://download.baderlab.org/EM_Genesets/`. 
+* gmt_BP: A list of class GMT, which is a curated human gene ontology  gene sets from the Bader Lab `https://download.baderlab.org/EM_Genesets/`. 
+* gmt_TF: A list of class GMT, which is a curated human transcription factor gene sets from the Bader Lab `https://download.baderlab.org/EM_Genesets/`. 
 * DEET_metadata: the same as the `metadata` dataframe (see above).
 
 #### DEET_feature_extract_input
@@ -210,7 +210,7 @@ Named list where each element contains 6 objects. Each object will contain the r
 
 * DEET_feature_extract expects three variables: a gene-by-comparison matrix populated with a statistic related to differential expresion (e.g., p-value, fold-change), a response variable (i.e., an output dependent variable), and a category.
 
-* mat - a gene-bycomparison matrix populated with a statistic related to differential expression. The matrix in `DEET_data_download()` is populated with the log2FC of genes if they were deemed as significant (padj < 0.05). Other matrices, namely those populated by p-value, fold-change, and t-statitic (including the matrices for all DEGs) can be found in `http://wilsonlab.org/public/DEET_data/feature_matrices` and can be downloaded separately.
+* mat - a gene-bycomparison matrix populated with a statistic related to differential expression. The matrix in `DEET_data_download()` is populated with the log2FC of genes if they were deemed as significant (padj < 0.05). Other matrices, namely those populated by p-value, fold-change, and t-statitic (including the matrices for all DEGs) can be found in `https://www.wilsonlab.org/public/DEET_data/feature_matrices` and can be downloaded separately.
 * respeonse: a character vector identifying each study, this can be categorical, binomial (e.g. 0/1, T/F), or continuous
 * datatype: a character indicating if the response is "binomial", "categorical", or "continuous". This is case sensitive.
 
@@ -335,7 +335,7 @@ As mentioned previously, the genesets within DEET are easily transferrable to ot
 
 #### Saving DEET gene set for GSEA, gprofiler, etc.
 
-One option is to download the *gmt files diretly from our ftp. `http://wilsonlab.org/public/DEET_data/DEET_DE.gmt` Is directly compatible with these tools.
+One option is to download the *gmt files diretly from our ftp. `https://www.wilsonlab.org/public/DEET_data/DEET_DE.gmt` Is directly compatible with these tools.
 
 The other option would be to save the downloaded DEET gmt as a gmt file. This is completed using the ActivePathways R package. Instead of using the example data as shown below, please use the full dataset.
 

diff --git a/inst/doc/DEET_vignette.html b/inst/doc/DEET_vignette.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Dustin Sokolowski" />
 
-<meta name="date" content="2023-08-16" />
+<meta name="date" content="2024-06-25" />
 
 <title>Differential Expression Enrichment Tool (DEET)</title>
 
@@ -341,7 +341,7 @@
 <h1 class="title toc-ignore">Differential Expression Enrichment Tool
 (DEET)</h1>
 <h4 class="author">Dustin Sokolowski</h4>
-<h4 class="date">2023-08-16</h4>
+<h4 class="date">2024-06-25</h4>
 
 
 <div id="TOC">
@@ -407,7 +407,7 @@ <h3>Installation</h3>
 <h2>Downloading files</h2>
 <p>All processed DEGs, metadata, and enriched pathways in formats
 compatible with this package as well as other methods such as gene set
-enrichment analysis are stored here: <a href="http://wilsonlab.org/public/DEET_data/" class="uri">http://wilsonlab.org/public/DEET_data/</a></p>
+enrichment analysis are stored here: <a href="https://www.wilsonlab.org/public/DEET_data/" class="uri">https://www.wilsonlab.org/public/DEET_data/</a></p>
 <p>No functions within DEET automatically load data for the user, so the
 data either needs to be downloaded directly from the ftp, or using the
 downloader function.</p>
@@ -478,10 +478,10 @@ <h4>DEET_enrich_input</h4>
 case the gene-set is the DEGs that are enriched within that study.</li>
 <li>gmt_BP: A list of class GMT, which is a curated human gene ontology
 gene sets from the Bader Lab
-<code>http://download.baderlab.org/EM_Genesets/</code>.</li>
+<code>https://download.baderlab.org/EM_Genesets/</code>.</li>
 <li>gmt_TF: A list of class GMT, which is a curated human transcription
 factor gene sets from the Bader Lab
-<code>http://download.baderlab.org/EM_Genesets/</code>.</li>
+<code>https://download.baderlab.org/EM_Genesets/</code>.</li>
 <li>DEET_metadata: the same as the <code>metadata</code> dataframe (see
 above).</li>
 </ul>
@@ -720,8 +720,8 @@ <h4>Inputs</h4>
 if they were deemed as significant (padj &lt; 0.05). Other matrices,
 namely those populated by p-value, fold-change, and t-statitic
 (including the matrices for all DEGs) can be found in
-<code>http://wilsonlab.org/public/DEET_data/feature_matrices</code> and
-can be downloaded separately.</p></li>
+<code>https://www.wilsonlab.org/public/DEET_data/feature_matrices</code>
+and can be downloaded separately.</p></li>
 <li><p>respeonse: a character vector identifying each study, this can be
 categorical, binomial (e.g. 0/1, T/F), or continuous</p></li>
 <li><p>datatype: a character indicating if the response is “binomial”,
@@ -882,7 +882,7 @@ <h3>Using DEET gene lists with other studies and enriching two input
 <div id="saving-deet-gene-set-for-gsea-gprofiler-etc." class="section level4">
 <h4>Saving DEET gene set for GSEA, gprofiler, etc.</h4>
 <p>One option is to download the *gmt files diretly from our ftp.
-<code>http://wilsonlab.org/public/DEET_data/DEET_DE.gmt</code> Is
+<code>https://www.wilsonlab.org/public/DEET_data/DEET_DE.gmt</code> Is
 directly compatible with these tools.</p>
 <p>The other option would be to save the downloaded DEET gmt as a gmt
 file. This is completed using the ActivePathways R package. Instead of

diff --git a/vignettes/DEET_vignette.Rmd b/vignettes/DEET_vignette.Rmd
@@ -48,7 +48,7 @@ devtools::install_github("wilsonlabgroup/DEET")
 
 ## Downloading files
 
-All processed DEGs, metadata, and enriched pathways in formats compatible with this package as well as other methods such as gene set enrichment analysis are stored here: http://wilsonlab.org/public/DEET_data/
+All processed DEGs, metadata, and enriched pathways in formats compatible with this package as well as other methods such as gene set enrichment analysis are stored here: https://www.wilsonlab.org/public/DEET_data/
 
 No functions within DEET automatically load data for the user, so the data either needs to be downloaded directly from the ftp, or using the downloader function.
 
@@ -87,8 +87,8 @@ This is the meat and potatoes of the DEET dataset. Here, you can find all of the
 * DEET_gmt_BP: A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the pathways that are enriched within that study.
 * DEET_gmt_TF: A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the TFs that are enriched within that study.
 * DEET_gmt_DE: A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the DEGs that are enriched within that study.
-* gmt_BP: A list of class GMT, which is a curated human gene ontology  gene sets from the Bader Lab `http://download.baderlab.org/EM_Genesets/`. 
-* gmt_TF: A list of class GMT, which is a curated human transcription factor gene sets from the Bader Lab `http://download.baderlab.org/EM_Genesets/`. 
+* gmt_BP: A list of class GMT, which is a curated human gene ontology  gene sets from the Bader Lab `https://download.baderlab.org/EM_Genesets/`. 
+* gmt_TF: A list of class GMT, which is a curated human transcription factor gene sets from the Bader Lab `https://download.baderlab.org/EM_Genesets/`. 
 * DEET_metadata: the same as the `metadata` dataframe (see above).
 
 #### DEET_feature_extract_input
@@ -210,7 +210,7 @@ Named list where each element contains 6 objects. Each object will contain the r
 
 * DEET_feature_extract expects three variables: a gene-by-comparison matrix populated with a statistic related to differential expresion (e.g., p-value, fold-change), a response variable (i.e., an output dependent variable), and a category.
 
-* mat - a gene-bycomparison matrix populated with a statistic related to differential expression. The matrix in `DEET_data_download()` is populated with the log2FC of genes if they were deemed as significant (padj < 0.05). Other matrices, namely those populated by p-value, fold-change, and t-statitic (including the matrices for all DEGs) can be found in `http://wilsonlab.org/public/DEET_data/feature_matrices` and can be downloaded separately.
+* mat - a gene-bycomparison matrix populated with a statistic related to differential expression. The matrix in `DEET_data_download()` is populated with the log2FC of genes if they were deemed as significant (padj < 0.05). Other matrices, namely those populated by p-value, fold-change, and t-statitic (including the matrices for all DEGs) can be found in `https://www.wilsonlab.org/public/DEET_data/feature_matrices` and can be downloaded separately.
 * respeonse: a character vector identifying each study, this can be categorical, binomial (e.g. 0/1, T/F), or continuous
 * datatype: a character indicating if the response is "binomial", "categorical", or "continuous". This is case sensitive.
 
@@ -335,7 +335,7 @@ As mentioned previously, the genesets within DEET are easily transferrable to ot
 
 #### Saving DEET gene set for GSEA, gprofiler, etc.
 
-One option is to download the *gmt files diretly from our ftp. `http://wilsonlab.org/public/DEET_data/DEET_DE.gmt` Is directly compatible with these tools.
+One option is to download the *gmt files diretly from our ftp. `https://www.wilsonlab.org/public/DEET_data/DEET_DE.gmt` Is directly compatible with these tools.
 
 The other option would be to save the downloaded DEET gmt as a gmt file. This is completed using the ActivePathways R package. Instead of using the example data as shown below, please use the full dataset.