update docs

slowkow · Apr 25, 2024 · bfa5356 · bfa5356
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hlabud
 Title: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA
-Version: 1.0.0.9999
+Version: 2.0.0
 Authors@R: c(
     person("Kamil", "Slowikowski", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2843-6370"))
     )

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,5 @@
-# hlabud 1.0.0.9999
+hlabud 2.0.0
+============
 
 ## Bug fixes
 
@@ -10,6 +11,8 @@
 
 ## Changes
 
+* Change position names from `pos21_D` to `D21`. When negative, `posn21_D` to `Dn21`.
+
 * Change `dosage()` to take a one-hot matrix as the first argument.
 
 * Change `dosage()` to return full allele names from IMGT when matching to partial allele names like `DRB1*03` or `DRB1*03:01`. And show messages indicating which alleles were matched when `verbose=TRUE`.
@@ -18,6 +21,10 @@
 
 * Automatically overwrite `{hlabud_dir}/tags.json` if it is older than 24 hours.
 
-# hlabud 1.0.0
+
+hlabud 1.0.0
+============
+
+* Initial release.
 
 * Added a `NEWS.md` file to track changes to the package.
diff --git a/man/dosage.Rd b/man/dosage.Rd
diff --git a/man/hla_alignments.Rd b/man/hla_alignments.Rd
diff --git a/man/hla_divergence.Rd b/man/hla_divergence.Rd
diff --git a/vignettes/articles/examples_files/figure-html/umap-2digit-1.png b/vignettes/articles/examples_files/figure-html/umap-2digit-1.png
diff --git a/vignettes/articles/examples_files/figure-html/umap-57-1.png b/vignettes/articles/examples_files/figure-html/umap-57-1.png
diff --git a/vignettes/articles/examples_files/figure-html/umap-D57-1.png b/vignettes/articles/examples_files/figure-html/umap-D57-1.png