LocToGeneName: LocToGeneName
In TomHarrop/oryzr: Work with Oryza sativa gene identifiers

Description Usage Arguments Details Value Examples

Convert MSU identifiers to CSGNL gene names and symbols and generate a label for plotting if requested.

1	LocToGeneName(LOCs, shortLabels = FALSE, return.synonyms = FALSE)

`LOCs`	Character vector of MSU locus identifiers
`shortLabels`	Boolean (default `FALSE`). Tries to return a sensible label e.g. for plotting: either the LOC_ID for unnamed genes or the name for named genes, with synonyms in brackets.
`return.synonyms`	Boolean (default `FALSE`). Return a long data.table including a column with the synonyms for each gene.

Conversion from MSU to Rap-DB identifiers uses the table of RAP-DB and MSU IDs available from Rap-DB. CSGNL symbols and gene names are retrieved from the OryzabaseGeneListEn database, downloaded from Oryzabase.

Returns a data.table with columns MsuID (MSUv7 gene identifier), RapID (RAP-DB gene identifier), symbols (CSGNL recommended symbol), names (CSGNL recommended name), MsuAnnotation (TIGR annotations), OgroObjective and OgroRef (manual annotation from OGRO database) and optionally labels for plotting. If return.synonyms is TRUE, returns a long data.table additionally containing columns symbol_synonyms and name_synonyms.

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LocToGeneName(c('LOC_Os01g03340', 'LOC_Os01g09410', 'LOC_Os01g17396', 'LOC_Os01g18800', 'LOC_Os01g44069', 'LOC_Os01g45470', 'LOC_Os01g53880', 'LOC_Os01g64730', 'LOC_Os01g71820', 'LOC_Os02g07110', 'LOC_Os02g26680', 'LOC_Os02g26700', 'LOC_Os02g41904', 'LOC_Os02g42880', 'LOC_Os02g44630', 'LOC_Os03g15530', 'LOC_Os03g22270', 'LOC_Os03g61160', 'LOC_Os04g58710', 'LOC_Os06g06750', 'LOC_Os07g32170', 'LOC_Os08g24930', 'LOC_Os08g31980', 'LOC_Os09g07154', 'LOC_Os09g25330', 'LOC_Os09g31438', 'LOC_Os10g07229', 'LOC_Os10g18870', 'LOC_Os10g26340', 'LOC_Os10g42210', 'LOC_Os10g42220'))
LocToGeneName(c('LOC_Os03g03034', 'LOC_Os06g36560', 'LOC_Os01g50910', "LOC_Os03g60430"))
LocToGeneName(c("LOC_Os01g03840", "LOC_Os01g10110", "LOC_Os01g10504", "LOC_Os01g40630", "LOC_Os01g61480", "LOC_Os01g66030", "LOC_Os01g66290", "LOC_Os02g15950", "LOC_Os02g45770", "LOC_Os02g52340", "LOC_Os03g11600", "LOC_Os03g11614", "LOC_Os03g51690", "LOC_Os03g54170", "LOC_Os03g57240", "LOC_Os03g60430", "LOC_Os04g32510", "LOC_Os04g49150", "LOC_Os04g51000", "LOC_Os05g41760", "LOC_Os06g11330", "LOC_Os06g45460", "LOC_Os06g49840", "LOC_Os06g50340", "LOC_Os07g13170", "LOC_Os07g15770", "LOC_Os07g41370", "LOC_Os07g42410", "LOC_Os07g47330", "LOC_Os08g06480", "LOC_Os08g07740", "LOC_Os08g39890", "LOC_Os08g41950", "LOC_Os09g26999", "LOC_Os09g32948", "LOC_Os10g33780", "LOC_Os11g38270", "LOC_Os12g10540"))