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Source  : 0cd0892
Branch  : main
Author  : Jason Williams <[email protected]>
Time    : 2025-12-15 16:42:52 +0000
Message : Merge pull request #326 from naupaka/main

Add links to descriptions of VCF; resolves #281

Author: actions-user

03-basics-factors-dataframes.md

@@ -183,6 +183,13 @@ a view of the data in a new tab.
 
 ![RStudio data frame view](fig/rstudio_dataframeview.png)
 
+The majority of the columns in the data frame correspond to standard fields found in a 
+*Variant Call Format (VCF)* file, while others were added during our data processing. The VCF 
+format is a standard format for storing variant calls (also known as Single Nucleotide Polymorphisms or SNPs),
+and you can read more about it, including a description of the fields we have here 
+in [the VCF specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf) 
+or [on wikipedia](https://en.wikipedia.org/wiki/Variant_Call_Format).
+
 We can also quickly query the dimensions of the variable using `dim()`. You'll see that the first number `801` shows the number of rows, then `29` the number of columns
 
 
@@ -687,17 +694,13 @@ install.packages("ggplot2")
 ```
 
 ``` output
-# Downloading packages -------------------------------------------------------
-- Downloading ggplot2 from https://packagemanager.posit.co/cran/__linux__/jammy/latest ... OK [8.1 Mb in 0.37s]
-Successfully downloaded 1 package in 1.5 seconds.
-
 The following package(s) will be installed:
 - ggplot2 [4.0.1]
 These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/linux-ubuntu-jammy/R-4.5/x86_64-pc-linux-gnu".
 
 # Installing packages --------------------------------------------------------
-- Installing ggplot2 ...                        OK [installed binary and cached in 1.1s]
-Successfully installed 1 package in 1.2 seconds.
+- Installing ggplot2 ...                        OK [linked from cache]
+Successfully installed 1 package in 5.9 milliseconds.
 ```
 
 ``` r
@@ -711,7 +714,7 @@ These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/
 
 # Installing packages --------------------------------------------------------
 - Installing dplyr ...                          OK [linked from cache]
-Successfully installed 1 package in 4.5 milliseconds.
+Successfully installed 1 package in 4.3 milliseconds.
 ```
 
 These two packages are among the most popular add on packages used in R, and they are part of a large set of very useful packages called the [tidyverse](https://www.tidyverse.org). Packages in the tidyverse are designed to work well together and are made to work with tidy data (which we described earlier in this lesson).

config.yaml

@@ -0,0 +1,88 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'dc'
+
+# Overall title for pages.
+title: 'Data Analysis and Visualization with R for Genomics'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: '2018-03-12'
+
+# Comma-separated list of keywords for the lesson
+keywords: 'software, data, lesson, The Carpentries'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'beta'
+
+# License of the lesson materials (recommended CC-BY 4.0)
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/datacarpentry/genomics-r-intro'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: '[email protected]'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes: 
+- 00-introduction.Rmd
+- 01-r-basics.Rmd
+- 02-data-prelude.Rmd
+- 03-basics-factors-dataframes.Rmd
+- 04-bioconductor-vcfr.Rmd
+- 05-dplyr.Rmd
+- 06-data-visualization.Rmd
+- 07-r-help.Rmd
+
+# Information for Learners
+learners: 
+
+# Information for Instructors
+instructors: 
+
+# Learner Profiles
+profiles: 
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+
+
+url: 'https://datacarpentry.github.io/genomics-r-intro'
+analytics: carpentries
+lang: en

md5sum.txt

@@ -6,7 +6,7 @@
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 "episodes/01-r-basics.Rmd" "cd2d5e1bef882767cb199933bdc080c4" "site/built/01-r-basics.md" "2025-12-10"
 "episodes/02-data-prelude.Rmd" "3c871c508670de40fd3b2a853d67e0aa" "site/built/02-data-prelude.md" "2025-12-10"
-"episodes/03-basics-factors-dataframes.Rmd" "8443a46ba31357bbccd110e025904b9f" "site/built/03-basics-factors-dataframes.md" "2025-12-10"
+"episodes/03-basics-factors-dataframes.Rmd" "36b39c099d6a7e2e774db064ce6b8d46" "site/built/03-basics-factors-dataframes.md" "2025-12-15"
 "episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2025-12-10"
 "episodes/05-dplyr.Rmd" "0eb40a1862a4acb0e68cfa2f89d28b2a" "site/built/05-dplyr.md" "2025-12-10"
 "episodes/06-data-visualization.Rmd" "b6a629582ef76b79ecabdd6aeb6df9b1" "site/built/06-data-visualization.md" "2025-12-10"