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Source  : 77a83ba
Branch  : main
Author  : Kevin Rue-Albrecht <kevinrue67@gmail.com>
Time    : 2024-05-15 12:41:43 +0000
Message : Adjust chapter about genomic ranges (#85)

* fix typo

* rephrase

* mention getter functions

* update challenge

07-genomic-ranges.md

@@ -537,8 +537,8 @@ GRanges object with 2 ranges and 0 metadata columns:
   seqinfo: 2 sequences from an unspecified genome; no seqlengths
 ```
 
-Finally, the examples above also demonstrate that `GRanges` objects include a
-component called `seqinfo`, which is occasionally used to store information
+Finally, the example above also demonstrate that `GRanges` objects include a
+component called `seqinfo`, which can be used to store information
 about each sequence that may be represented in the `seqnames` component.
 In the latest example above, we have not provide any information about any
 sequence.
@@ -587,6 +587,61 @@ GRanges object with 2 ranges and 0 metadata columns:
   seqinfo: 2 sequences (1 circular) from homo_sapiens genome
 ```
 
+The start and end positions of the individual ranges as well as the width of
+every interval can be extracted as numeric vector using the functions `start()`,
+`end()` and `width()`, respectively.
+
+
+``` r
+start(demo_granges2)
+```
+
+``` output
+[1] 10 20
+```
+
+``` r
+end(demo_granges2)
+```
+
+``` output
+[1] 25 35
+```
+
+``` r
+width(demo_granges2)
+```
+
+``` output
+[1] 16 16
+```
+
+The sequence names and strand information can be extracted using the functions
+`seqnames()` and `strand()`, respectively.
+
+
+``` r
+seqnames(demo_granges2)
+```
+
+``` output
+factor-Rle of length 2 with 2 runs
+  Lengths:    1    1
+  Values : chr1 chr2
+Levels(2): chr1 chr2
+```
+
+``` r
+strand(demo_granges2)
+```
+
+``` output
+factor-Rle of length 2 with 2 runs
+  Lengths: 1 1
+  Values : + -
+Levels(3): + - *
+```
+
 ### Metadata on GRanges
 
 Similarly to `IRanges`, metadata can be passed directly to the `GRanges`
@@ -877,10 +932,13 @@ ENST00000676189 ENST00000676319 ENST00000676397
 
 Importantly, the function `lengths()` (with a final `s`) demonstrated above
 is different from the function `length()` (without `s`).
-The former is meant to be used on list objects, while the latter is meant
-to be used on vectors.
+The former is meant to be used on list objects, returning a vector giving the
+length of each element in the list; while the latter returns a single numeric
+scalar giving the length of the list itself (i.e., the number of elements
+in the list).
 
-What does `length(actb_exons_by_transcript)` return, and why?
+What does `length(actb_exons_by_transcript)` return, and what does this
+number represent biologically?
 
 :::::::::::::::  solution
 

config.yaml

@@ -0,0 +1,85 @@
+#------------------------------------------------------------
+# 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: 'incubator'
+
+# Overall title for pages.
+title: 'The Bioconductor project'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: '2020-09-14'
+
+# 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: 'pre-alpha'
+
+# License of the lesson
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/carpentries-incubator/bioc-project'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: 'team@carpentries.org'
+
+# 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: 
+- 01-setup.Rmd
+- 02-introduction-to-bioconductor.Rmd
+- 03-installing-bioconductor.Rmd
+- 04-getting-help.Rmd
+- 05-s4.Rmd
+- 06-biological-sequences.Rmd
+- 07-genomic-ranges.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://carpentries-incubator.github.io/bioc-project'

md5sum.txt

@@ -9,7 +9,7 @@
 "episodes/04-getting-help.Rmd" "ef95b83e2cf1db86786c9b8ff971684b" "site/built/04-getting-help.md" "2024-05-15"
 "episodes/05-s4.Rmd" "e97eed7893703ad409eb937d95e357b1" "site/built/05-s4.md" "2024-05-15"
 "episodes/06-biological-sequences.Rmd" "da5a66034d8bba99de8f7746584a7c95" "site/built/06-biological-sequences.md" "2024-05-15"
-"episodes/07-genomic-ranges.Rmd" "1678d11e207781b420e36810e603000b" "site/built/07-genomic-ranges.md" "2024-05-15"
+"episodes/07-genomic-ranges.Rmd" "a88d289c2db16b377d3af09a9c896086" "site/built/07-genomic-ranges.md" "2024-05-15"
 "instructors/instructor-notes.md" "a848c3b904c16f0840e7ec385de58d7d" "site/built/instructor-notes.md" "2024-05-15"
 "learners/discuss.md" "90557a59d285aa7ce2a8adfc5799b1a8" "site/built/discuss.md" "2024-05-15"
 "learners/reference.md" "c0ac274d8350e94fbaef3e28b458c7f4" "site/built/reference.md" "2024-05-15"