Update v04_uploading_a_Trio.rmd

Author: littlecabiria

vignettes/v04_uploading_a_Trio.rmd

@@ -1,92 +1,97 @@
----
-title: "4 Uploading a Trio to Curated Trio Datasets"
-author: "BenchHub Team"
-date: "`r Sys.Date()`"
-output: BiocStyle::html_document
-vignette: >
-  %\VignetteIndexEntry{4 Upload Trio class}
-  %\VignetteEncoding{UTF-8}
-  %\VignetteEngine{knitr::rmarkdown}
----
-
-# Instructions for Uploading a Trio to Curated Trio Datasets
-
-This guide provides step-by-step instructions for uploading a Trio object to the [Curated Trio Datasets sheet](https://docs.google.com/spreadsheets/d/1zEyB5957aXYq6LvI9Ma65Z7GStpjIDWL16frru73qiY/edit). Curated Trio Dataset is a list of datasets with proven utility. It includes creating a GitHub Personal Access Token (PAT) with gist write access and uploading data to Figshare.
-
-
-## Step 1: Create a GitHub Personal Access Token (PAT)
-
-To upload metrics as a GitHub Gist, you need a GitHub PAT with gist write access.
-
-1. Log in to your GitHub account.
-2. Navigate to **Settings** > **Developer settings** > **Personal access tokens** > **Tokens (classic)**.
-3. Click **Generate new token**.
-4. Select the following scopes:
-   - `gist` (for creating and managing gists)
-5. Click **Generate token** and copy the token.
-
-### Set the PAT in R
-Add the token to your environment in R:
-
-```r
-Sys.setenv(GITHUB_PAT = "your_personal_access_token")
-```
-
-Replace `"your_personal_access_token"` with the token you copied.
-
-### Ensure `googlesheets4` is set up
-
-1. Install the `googlesheets4` package if you haven't already:
-   ```r
-   install.packages("googlesheets4")
-   ```
-2. Authenticate with your Google account:
-   ```r
-   googlesheets4::gs4_auth()
-   ```
-
-
-## Step 2: Add the Trio to Curated Trio Datasets
-
-1. In R, create a `Trio` object and ensure it is properly populated with data, supporting evidence, and metrics.
-2. Use the `writeCTD()` method to upload the Trio metadata to the Curated Trio Datasets sheet:
-
-```r
-trio$writeCTD(name = "Your Dataset Name")
-```
-
-3. Follow the prompts to:
-   - Save the dataset and supporting evidence locally (optional).
-   - Provide the Figshare URL. For more detailed instructions on uploading to Figshare, see below.
-   - Select the data type (e.g., omics, clinical, spatial, other).
-   - Confirm the upload of supporting evidence to Figshare.
-
-
-
-## Step 3: Verify the Upload
-
-1. Check the Curated Trio Datasets Google Sheet to ensure your dataset has been added:
-   [Curated Trio Datasets](https://docs.google.com/spreadsheets/d/1zEyB5957aXYq6LvI9Ma65Z7GStpjIDWL16frru73qiY/)
-
-2. Verify that the metrics have been uploaded as a GitHub Gist.
-
-
-
-## Notes
-
-- Ensure you have an active internet connection during the upload process.
-- If you encounter any issues, check that your GitHub PAT and Figshare URL are correctly set.
-
-### Uploading Data to Figshare
-
-1. Log in to your Figshare account.
-2. Click **Create a new item**.
-3. Fill in the required metadata fields (e.g., title, description, tags).
-4. Upload your dataset files (e.g., `.rds` files for the dataset and supporting evidence). 
-   - NOTE: `writeCTD` can create the
-5. Publish the item to make it publicly accessible.
-6. Copy the Figshare URL of the published item.
-
-
-
-Happy uploading!
+---
+title: "4 Uploading a Trio to Curated Trio Datasets"
+author: "BenchHub Team"
+date: "`r Sys.Date()`"
+output: BiocStyle::html_document
+vignette: >
+  %\VignetteIndexEntry{4 Upload Trio class}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+---
+
+# Instructions for Uploading a Trio to Curated Trio Datasets
+
+This guide provides step-by-step instructions for uploading a Trio object to the [Curated Trio Datasets sheet](https://docs.google.com/spreadsheets/d/1zEyB5957aXYq6LvI9Ma65Z7GStpjIDWL16frru73qiY/edit). Curated Trio Dataset is a list of datasets with proven utility. It includes creating a GitHub Personal Access Token (PAT) with gist write access and uploading data to Figshare.
+
+
+## Step 1: Create a GitHub Personal Access Token (PAT)
+
+To upload metrics as a GitHub Gist, you need a GitHub PAT with gist write access.
+
+1. Log in to your GitHub account.
+2. Navigate to **Settings** > **Developer settings** > **Personal access tokens** > **Tokens (classic)**.
+3. Click **Generate new token**.
+4. Select the following scopes:
+   - `gist` (for creating and managing gists)
+5. Click **Generate token** and copy the token.
+
+### Set the PAT in R
+Add the token to your environment in R:
+
+```r
+Sys.setenv(GITHUB_PAT = "your_personal_access_token")
+```
+
+Replace `"your_personal_access_token"` with the token you copied.
+
+### Ensure `googlesheets4` is set up
+
+1. Install the `googlesheets4` package if you haven't already:
+   ```r
+   install.packages("googlesheets4")
+   ```
+2. Authenticate with your Google account:
+   ```r
+   googlesheets4::gs4_auth()
+   ```
+
+
+## Step 2: Add the Trio to Curated Trio Datasets
+
+1. In R, create a `Trio` object and ensure it is properly populated with data, supporting evidence, and metrics.
+2. Use the `writeCTD()` method to upload the Trio metadata to the Curated Trio Datasets sheet:
+
+```r
+trio$writeCTD(name = "Your Dataset Name")
+```
+
+3. Follow the prompts to:
+   - Save the dataset and supporting evidence locally (optional).
+   - Provide the Figshare URL. For more detailed instructions on uploading to Figshare, see below.
+   - Select the data type (e.g., omics, clinical, spatial, other).
+   - Confirm the upload of supporting evidence to Figshare.
+
+
+
+## Step 3: Verify the Upload
+
+1. Check the Curated Trio Datasets Google Sheet to ensure your dataset has been added:
+   [Curated Trio Datasets](https://docs.google.com/spreadsheets/d/1zEyB5957aXYq6LvI9Ma65Z7GStpjIDWL16frru73qiY/)
+
+2. Verify that the metrics have been uploaded as a GitHub Gist.
+
+
+
+## Notes
+
+- Ensure you have an active internet connection during the upload process.
+- If you encounter any issues, check that your GitHub PAT and Figshare URL are correctly set.
+
+### Uploading Data to Figshare
+
+1. Log in to your Figshare account.
+2. Click **Create a new item**.
+3. Fill in the required metadata fields (e.g., title, description, tags).
+4. Upload your dataset files (e.g., `.rds` files for the dataset and supporting evidence). 
+   - NOTE: `writeCTD` can create the
+5. Publish the item to make it publicly accessible.
+6. Copy the Figshare URL of the published item.
+
+
+Happy uploading!
+
+# Session Info
+
+```{r}
+sessionInfo()
+```