Merge pull request #23 from stephenturner/grch3738

Use https in host, fix GRCh37 vs 38

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: annotables
 Type: Package
 Title: Ensembl Annotation Tables
-Version: 0.1.91
+Version: 0.2.0
 Authors@R: c(
     person("Stephen", "Turner",
            email = "[email protected]",
@@ -17,6 +17,7 @@ URL: https://github.com/stephenturner/annotables
 BugReports: https://github.com/stephenturner/annotables/issues
 License: GPL-3
 LazyData: TRUE
+LazyDataCompression: xz
 Depends:
     R (>= 3.1.2)
 Imports: tibble
@@ -29,4 +30,4 @@ Suggests:
     whisker,
     yaml
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.0.1
+RoxygenNote: 7.2.3

NEWS.md

@@ -0,0 +1,4 @@
+# v0.2.0
+
+- Added host to data retrieval function
+- Updated all recipes to use https

R/utils.R

@@ -1,7 +1,7 @@
 # Generate annotable documentation based on recipe
 document_annotable <- function(x, table, type) {
   type <- match.arg(type, c("gene", "tx2gene"))
-  template.path <- system.file("inst/templates",
+  template.path <- system.file("templates",
                                paste0(type, ".R"),
                                package = "annotables",
                                mustWork = TRUE)

README.Rmd

@@ -12,71 +12,46 @@ knitr::opts_chunk$set(
 library(annotables)
 ```
 
-[airway]: https://bioconductor.org/packages/release/data/experiment/html/airway.html
-[biobroom]: http://www.bioconductor.org/packages/devel/bioc/html/biobroom.html
-[Bioconductor]: https://bioconductor.org
-[biomaRt]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html
-[DESeq2]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
-[devtools]: https://cran.r-project.org/package=devtools
-[dplyr]: http://dplyr.tidyverse.org
-[R]: https://www.r-project.org
-[tibble]: http://tibble.tidyverse.org
-
-
 [![DOI](https://zenodo.org/badge/3882/stephenturner/annotables.svg)](https://zenodo.org/badge/latestdoi/3882/stephenturner/annotables)
 
 Provides tables for converting and annotating Ensembl Gene IDs.
 
-
 ## Installation
 
-This is an [R][] package.
-
-### [Bioconductor][] method
-
-```{r, eval=FALSE}
-source("https://bioconductor.org/biocLite.R")
-biocLite("stephenturner/annotables")
-```
-
-### [devtools][] method
-
 ```{r, eval=FALSE}
 install.packages("devtools")
 devtools::install_github("stephenturner/annotables")
 ```
 
-
 ## Rationale
 
-Many bioinformatics tasks require converting gene identifiers from one convention to another, or annotating gene identifiers with gene symbol, description, position, etc. Sure, [biomaRt][] does this for you, but I got tired of remembering biomaRt syntax and hammering Ensembl's servers every time I needed to do this.
+Many bioinformatics tasks require converting gene identifiers from one convention to another, or annotating gene identifiers with gene symbol, description, position, etc. Sure, [biomaRt](https://bioconductor.org/packages/release/bioc/html/biomaRt.html) does this for you, but I got tired of remembering biomaRt syntax and hammering Ensembl's servers every time I needed to do this.
 
 This package has basic annotation information from **`r ensembl_version`** for:
 
-- Human build 38 (`grch38`)
-- Human build 37 (`grch37`)
-- Mouse (`grcm38`)
-- Rat (`rnor6`)
-- Chicken (`galgal5`)
-- Worm (`wbcel235`)
-- Fly (`bdgp6`)
-- Macaque (`mmul801`)
+-   Human build 38 (`grch38`)
+-   Human build 37 (`grch37`)
+-   Mouse (`grcm38`)
+-   Rat (`rnor6`)
+-   Chicken (`galgal5`)
+-   Worm (`wbcel235`)
+-   Fly (`bdgp6`)
+-   Macaque (`mmul801`)
 
 Where each table contains:
 
-- `ensgene`: Ensembl gene ID
-- `entrez`: Entrez gene ID
-- `symbol`: Gene symbol
-- `chr`: Chromosome
-- `start`: Start
-- `end`: End
-- `strand`: Strand
-- `biotype`: Protein coding, pseudogene, mitochondrial tRNA, etc.
-- `description`: Full gene name/description
+-   `ensgene`: Ensembl gene ID
+-   `entrez`: Entrez gene ID
+-   `symbol`: Gene symbol
+-   `chr`: Chromosome
+-   `start`: Start
+-   `end`: End
+-   `strand`: Strand
+-   `biotype`: Protein coding, pseudogene, mitochondrial tRNA, etc.
+-   `description`: Full gene name/description
 
 Additionally, there are `tx2gene` tables that link Ensembl gene IDs to Ensembl transcript IDs.
 
-
 ## Usage
 
 ```{r, eval=FALSE}
@@ -95,7 +70,7 @@ Look at the human genes-to-transcripts table:
 grch38_tx2gene
 ```
 
-Tables are saved in [tibble][] format, pipe-able with [dplyr][]:
+Tables are saved in [tibble](http://tibble.tidyverse.org) format, pipe-able with [dplyr](http://dplyr.tidyverse.org):
 
 ```{r, results='asis'}
 grch38 %>% 
@@ -105,8 +80,7 @@ grch38 %>%
     knitr::kable(.)
 ```
 
-
-Example with [DESeq2][] results from the [airway][] package, made tidy with [biobroom][]:
+Example with [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) results from the [airway](https://bioconductor.org/packages/release/data/experiment/html/airway.html) package, made tidy with [biobroom](http://www.bioconductor.org/packages/devel/bioc/html/biobroom.html):
 
 ```{r}
 library(DESeq2)