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Source  : 3d5460c
Branch  : main
Author  : Naupaka Zimmerman <[email protected]>
Time    : 2024-12-09 23:12:53 +0000
Message : Merge pull request #304 from ytakemon/rbasics_issues

Working pull request to address remaining rbasics issues

Author: actions-user

01-r-basics.md

@@ -144,6 +144,27 @@ In the 'Environment' window you will also get a table:
 The 'Environment' window allows you to keep track of the objects you have
 created in R.
 
+
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Tip: Use of white space for readability
+
+The white spaces surrounding the assignment operator `<-` in the example 
+above (`first_value <- 1`) are unnecessary. However, including them does make your code 
+easier to read. There are several style guides you can follow, and choosing 
+one is up to you, but consistency is key!
+
+A style guide we recommend is the Tidyverse [style guide](https://style.tidyverse.org/). 
+
+As they say:
+
+"Good coding style is like correct punctuation: you can manage without it, butitsuremakesthingseasiertoread."
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+
+
 :::::::::::::::::::::::::::::::::::::::  challenge
 
 ## Exercise: Create some objects in R
@@ -193,8 +214,9 @@ Here are some important details about naming objects in R.
   a colored highlight or RStudio gives you a suggested autocompletion you have
   chosen a name that has a reserved meaning.
 - **Use the recommended assignment operator**: In R, we use '\<- ' as the
-  preferred assignment operator. '=' works too, but is most commonly used in
-  passing arguments to functions (more on functions later). There is a shortcut
+  preferred assignment operator, which is recommended by the Tidyverse 
+  [style guide](https://style.tidyverse.org/) discussed above. '=' works too, but is most 
+  commonly used in passing arguments to functions (more on functions later). There is a shortcut
   for the R assignment operator:
   - Windows execution shortcut: <KBD>Alt</KBD>\+<KBD>\-</KBD>
   - Mac execution shortcut: <KBD>Option</KBD>\+<KBD>\-</KBD>
@@ -900,16 +922,19 @@ the vector you are searching:
 # current value of 'snp_genes':
 # chr [1:7] "OXTR" "ACTN3" "AR" "OPRM1" "CYP1A1" NA "APOA5"
 
-# test to see if "ACTN3" or "APO5A" is in the snp_genes vector
+# test to see if "ACTN3", "APO5A", or "actn3" is in the snp_genes vector
 # if you are looking for more than one value, you must pass this as a vector
 
-c("ACTN3","APOA5") %in% snp_genes
+c("ACTN3","APOA5", "actn3") %in% snp_genes
 ```
 
 ``` output
-[1] TRUE TRUE
+[1]  TRUE  TRUE FALSE
 ```
 
+Notice that the gene "actn3" is FALSE? This is because character vectors are case sensitive, so
+keep this in mind when subsetting and selecting values from a character vector. 
+
 :::::::::::::::::::::::::::::::::::::::::  callout
 
 ## Tip: What's the difference between the `%in% and the `==` operators?

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: 'Intro to R and RStudio 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

@@ -4,7 +4,7 @@
 "config.yaml" "b91cd97fa3b408bd1ac0a00e67ab3219" "site/built/config.yaml" "2024-12-03"
 "index.md" "7f9c30e6487338a0c3f8ecc4018873ab" "site/built/index.md" "2024-12-03"
 "episodes/00-introduction.Rmd" "03f55a33cafd3e5f3b407315c509a389" "site/built/00-introduction.md" "2024-12-03"
-"episodes/01-r-basics.Rmd" "b45f835c7d4314da15066f1f2cb86b21" "site/built/01-r-basics.md" "2024-12-03"
+"episodes/01-r-basics.Rmd" "01744c322b706b658550627e5a7fa4c3" "site/built/01-r-basics.md" "2024-12-09"
 "episodes/02-data-prelude.Rmd" "ab2b1fd3cdaae919f9e409f713a0a8ad" "site/built/02-data-prelude.md" "2024-12-03"
 "episodes/03-basics-factors-dataframes.Rmd" "0bb7c8d7807eea75f14ce8ca3d22febf" "site/built/03-basics-factors-dataframes.md" "2024-12-03"
 "episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2024-12-03"