| ... | ... |
@@ -14,7 +14,8 @@ Description: Functional enrichment from a list of features (genes, proteins, etc |
| 14 | 14 |
BioPlanet, Reactome and WikiPathways. Once downloaded, data are converted into |
| 15 | 15 |
a format allowing for fast enrichment analysis. |
| 16 | 16 |
URL: https://github.com/bartongroup/fenr |
| 17 |
-Depends: R (>= 4.1.0) |
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| 17 |
+BugReports: https://github.com/bartongroup/fenr/issues |
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| 18 |
+Depends: R (>= 4.2.0) |
|
| 18 | 19 |
License: MIT + file LICENSE |
| 19 | 20 |
Encoding: UTF-8 |
| 20 | 21 |
biocViews: |
| ... | ... |
@@ -6,14 +6,14 @@ |
| 6 | 6 |
- replacing url_exists with RCurl::url.exists |
| 7 | 7 |
- added NEWS.md |
| 8 | 8 |
|
| 9 |
-## Version 0.1.6 |
|
| 9 |
+## Version 0.1.6 (2022-08-23) |
|
| 10 | 10 |
|
| 11 | 11 |
- bug fix in fetch_kegg |
| 12 | 12 |
- removed `min_count` and `fdr_limit` arguments from `functional_enrichment`; filtering can be done afterwards |
| 13 | 13 |
- added a small Shiny app as an example of `fenr` |
| 14 | 14 |
- updates to vignette |
| 15 | 15 |
|
| 16 |
-## Version 0.1.7 |
|
| 16 |
+## Version 0.1.7 (2022-09-01) |
|
| 17 | 17 |
|
| 18 | 18 |
- small fixes |
| 19 | 19 |
- link to a separate GitHub Shiny app added |
| ... | ... |
@@ -21,24 +21,24 @@ |
| 21 | 21 |
- improved robustness |
| 22 | 22 |
- more tests |
| 23 | 23 |
|
| 24 |
- ## Version 0.1.8 |
|
| 24 |
+ ## Version 0.1.8 (2022-09-06) |
|
| 25 | 25 |
|
| 26 | 26 |
- `fetch_reactome` provides two ways of retrieving data, via one downloadable file or via APIs |
| 27 | 27 |
|
| 28 |
- ## Version 0.1.9 |
|
| 28 |
+ ## Version 0.1.9 (2022-09-13) |
|
| 29 | 29 |
|
| 30 | 30 |
- Replacing ontologyIndex::get_ontology with a simpler parser |
| 31 | 31 |
- Replacing KEGGREST with own simple API parsers |
| 32 | 32 |
- Applying BiocStyle to the vignette |
| 33 | 33 |
- improving test_functional_enrichment |
| 34 | 34 |
|
| 35 |
-## Version 0.1.10 |
|
| 35 |
+## Version 0.1.10 (2022-10-04) |
|
| 36 | 36 |
|
| 37 | 37 |
- Style changes for BiocCheck |
| 38 | 38 |
- Adding more tests |
| 39 | 39 |
- Fixing a bug in `parse_kegg_genes` |
| 40 | 40 |
|
| 41 |
- ## Version 0.1.11 |
|
| 41 |
+ ## Version 0.1.11 (2022-10-11) |
|
| 42 | 42 |
|
| 43 | 43 |
- Significant speed-up of enrichment by using Rfast::Hash in place of R lists |
| 44 | 44 |
- KEGG improvements, recognizing flat file genes with no gene synonym |
| ... | ... |
@@ -50,21 +50,21 @@ |
| 50 | 50 |
- Added functions `get_term_features` and `get_feature_terms` to access data safely |
| 51 | 51 |
- HACK: BioPlanet server's SSL certificate expired, so need insecure download. |
| 52 | 52 |
|
| 53 |
-## Version 0.1.14 |
|
| 53 |
+## Version 0.1.14 (2023-02-02) |
|
| 54 | 54 |
|
| 55 | 55 |
- Ditched large and clunky `Rfast` and using native R environments as fast hashes (see https://riptutorial.com/r/example/18339/environments-as-hash-maps) |
| 56 | 56 |
- A few tweaks and improvements |
| 57 | 57 |
|
| 58 |
-## Version 0.1.15 |
|
| 58 |
+## Version 0.1.15 (2023-03-02) |
|
| 59 | 59 |
|
| 60 | 60 |
- Fixed a bug where there are some features at a term that are not present in the universe (all features). This could happen when the universe was particularly small. Potentially a serious bug. |
| 61 | 61 |
|
| 62 |
-## Version 0.1.16 |
|
| 62 |
+## Version 0.1.16 (2023-03-16) |
|
| 63 | 63 |
|
| 64 | 64 |
- Added a fix to work correctly with integer feature IDs. |
| 65 | 65 |
|
| 66 | 66 |
|
| 67 |
-## Version 0.1.17 |
|
| 67 |
+## Version 0.1.17 (2023-04-18) |
|
| 68 | 68 |
|
| 69 | 69 |
- New units tests added |
| 70 | 70 |
|
| ... | ... |
@@ -96,7 +96,7 @@ prepare_for_enrichment <- function(terms, mapping, all_features = NULL, feature_ |
| 96 | 96 |
|
| 97 | 97 |
# Hash to select term name |
| 98 | 98 |
term2name <- new.env(hash = TRUE) |
| 99 |
- for (i in 1:nrow(terms)) {
|
|
| 99 |
+ for (i in seq_len(nrow(terms))) {
|
|
| 100 | 100 |
r <- terms[i, ] |
| 101 | 101 |
term2name[[r$term_id]] <- r$term_name |
| 102 | 102 |
} |
| ... | ... |
@@ -18,7 +18,7 @@ parse_obo_file <- function(obo) {
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| 18 | 18 |
blanks <- c(blanks, length(obo) + 1) |
| 19 | 19 |
|
| 20 | 20 |
# End lines: ignore empty lines beyond terms |
| 21 |
- ends <- blanks[1:length(starts)] |
|
| 21 |
+ ends <- blanks[seq_len(length(starts))] |
|
| 22 | 22 |
|
| 23 | 23 |
# Parse each term |
| 24 | 24 |
purrr::map2_dfr(starts, ends, function(i1, i2) {
|
