Ran github actions

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: transmogR
 Type: Package
 Title: Modify a set of reference sequences using a set of variants
-Version: 0.1.8
+Version: 0.99.0
 Authors@R: person("Stevie", "Pederson", 
     email = "stephen.pederson.au@gmail.com", 
     role = c("aut", "cre"),

R/transmogR-package.R

@@ -0,0 +1,35 @@
+#' transmogR: Create a variant-modified reference transcriptome
+#'
+#' The package `transmogR` has been designed for creation of a variant-modified
+#' reference transcriptome
+#'
+#' The package `transmogR` provides two primary functions for modifying complete
+#' transcriptomes or genomes:
+#'
+#' * [transmogrify()] for incorporating the supplied variants into
+#' transcriptomic sequences, and
+#' * [genomogrify()] for incorporating the supplied variants into genomic
+#' sequences, ideally to be passed as decoy sequences to a tool such as `salmon`.
+#'
+#' The main functions rely on lower-level functions such as:
+#'
+#' * [owl()] which over-writes letters (i.e. SNPs) within a sequence, and
+#' * [indelcator()] which incorporates InDels into an individual sequence
+#'
+#' Additional utility functions are provided which allow characterisation and
+#' exploration of any set of variants:
+#'
+#' * [overlapsByVar()] counts the variants which overlap sets of GenomicRanges,
+#' first splitting the variants into SNV, Insertions and Deletions
+#' * [parY()] returns the pseudo-autosomal regions for a chosen genome build as
+#' a GenomicRanges object
+#' * [upsetVarByCol()] produces an UpSet plot counting how many unique IDs are
+#' impacted by a set o variants. IDs can represent any column in the supplied
+#' ranges, such as gene_id or transcript_id
+#' * [varTypes()] classifies a set of variants into SNV, Insertions of Deletions
+#'
+#' @author
+#' Stevie Pederson
+#'
+#' @keywords internal
+"_PACKAGE"

README.md

@@ -7,9 +7,26 @@
 <!-- badges: end -->
 
 
-This package contains functions for creating a variant-modified, or mogrified, 
-reference genome or transcriptome.
+This package contains functions for creating a variant-modified reference genome or transcriptome.
 SNPs, Insertions and Deletions are all supported.
 
 With a generous tip of the hat and deep appreciation to Bill Watterson. 
 Results are expected to be more predictable than for prototype transmogrifiers.
+
+To install the stable version of `transmogR` from Bioconductor please try the following.
+
+```r
+if (!require("BiocManager")) {
+  install.packages("BiocManager")
+}
+BiocManager::install("transmogR")
+```
+
+Alternatively, the latest build can be installed using
+
+```r
+if (!require("BiocManager")) {
+  install.packages("BiocManager")
+}
+BiocManager::install("smped/transmogR")
+```

vignettes/creating_a_new_reference.Rmd

@@ -7,7 +7,9 @@ author:
 package: transmogR
 bibliography: '`r system.file("references.bib", package = "transmogR")`'
 output:
-  BiocStyle::html_document
+  BiocStyle::html_document:
+    toc: true
+    toc_depth: 2
 abstract: |
   The use of personalised or population-level variants opens the door to the 
   possibility of creating a variant-modified reference genome, or transcriptome.
@@ -52,7 +54,7 @@ require installation.
 if (!"BiocManager" %in% rownames(installed.packages()))
   install.packages("BiocManager")
 pkg <- c(
-  "rtracklayer", "BSgenome.Hsapiens.UCSC.hg38", "extraChIPs", "smped/transmogR"
+  "rtracklayer", "BSgenome.Hsapiens.UCSC.hg38", "extraChIPs", "transmogR"
 )
 BiocManager::install(pkg, update = FALSE)
 ```