Package: convertid 0.3.0
Vidal Fey
convertid: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.
Authors:
convertid_0.3.0.tar.gz
convertid_0.3.0.tar.gz(r-4.7-any)convertid_0.3.0.tar.gz(r-4.6-any)
convertid_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
convertid/json (API)
| # Install 'convertid' in R: |
| install.packages('convertid', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:018b4fc22a. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 436 | ||
| source / vignettes | OK | 278 | ||
| linux-release-x86_64 | OK | 316 | ||
| wasm-release | OK | 169 |
Exports:convert.aliasconvert.bmconvertId2get.bmlikely_symboltodisp2unify_gene_ids
Dependencies:AnnotationDbiaskpassassertthatBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRcpprlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrxml2XVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add values to cache | .addToCache |
| Check whether value in cache exists | .checkInCache |
| Read values from cache | .readFromCache |
| Convert Symbols to Aliases and Vice Versa. | convert.alias |
| Retrieve Additional Annotations from Biomart | convert.bm |
| Convert Gene Symbols to Ensembl Gene IDs or vice versa | convertId2 |
| Make a Query to Biomart. | get.bm |
| Retrieve Symbol Aliases and Previous symbols to determine a likely current symbol | likely_symbol |
| Convenience Function to Convert Ensembl Gene IDs to Gene Symbols | todisp2 |
| Unify gene IDs from BioMart and AnnotationDbi lookups | unify_gene_ids |