# HGNChelper
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## Changes in version 0.8.1
* Important bugfix: outdated symbols in extdata/mog_map.csv - those
  mogrified by Excel - were not being corrected. e.g. these
  corrections now work: MARC1 -> MTARC1, MARCH6 -> MARCHF6). Thank you
  to Richard Heery for the bug report.
* checkGeneSymbols() now returns a message with the date that maps in
  the package were last updated
* Built-in maps updated to Oct 23 2019

## Changes in version 0.7.0
* Use new genenames.org download URL (ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt)
* This includes non-coding RNA, "phenotype", pseudogene, protein-coding gene, and "other"

## Changes in version 0.6.0
* Add vignette

## Changes in version 0.5.0
* Add getCurrentHumanMap and getCurrentMouseMap

## Changes in version 0.4.2
* Support for checking mouse symbols added. See ?checkGeneSymbols and ?mouse.table

## Changes in version 0.3.2
* update map to Jan 17, 2016
* Fixed issue #4 
  (https://bitbucket.org/lwaldron/hgnchelper/issues/4/typos-in-mog_mapcsv)

## Changes in version 0.3.1
* update map to Dec 3, 2014
* fixed corner case of orf with incorrect capitalization - was being
identified as invalid, but not corrected.  Example was c21orf62-as1,
which now gets corrected to C21orf62-AS1 - see tests/checkGeneSymbols.R.

## Changes in version 0.3.0
* add toupper() to hgnc.table[, 1]
* add additional Excel date formats to inst/extdata/mog_map.csv
* additional unit tests in man/checkGeneSymbols.Rd

## Changes in version 0.2.6
* fixed checkGeneSymbols(x) when x contains NAs.

## Changes in version 0.2.5
* update inst/hgncLookup.R to new genenames.org webpage.
* added hgnc.table argument to checkGeneSymbols() to allow optional
  specification of a more up-to-date map from genenames.org.
* update to 2014/02/09 HGNC data.
* move vignette to new location
* GEO GPL analysis to inst/analyses, not included in build.

## Changes in version 0.2.2
* license to GPL >= 2.0 (from GPL > 2.0)
* convert all putative gene symbols to upper-case, except for orf. 
This catches symbols that are non-standard because of lower-case letters.
* added inst/extdata/genenames_org.csv for full transparency

## Changes in version 0.2.1
* changes to checkGeneSymbols:
    + Added unmapped.as.na option
    + set stringsAsFactors=FALSE so output columns are character class instead of factor
    + use return(df) instead of invisible(df).

## Changes in version 0.2
* Markus added checkGeneSymbols and unit tests.

## Changes in version 0.1
* Initial version uploaded to CRAN