SearchByGeneSymbol: SearchByGeneSymbol

In TomHarrop/oryzr: Work with Oryza sativa gene identifiers

Description

Search Rap-DB and oryzabase information by gene symbol and return identifiers for potential matches.

Usage

SearchByGeneSymbol(GeneSymbols, shortLabels = FALSE,
  return.synonyms = FALSE)

Arguments

shortLabels	Boolean (default FALSE). Tries to return a sensible label e.g. for plotting. See help for LocToRefSeq for more information.
return.synonyms	Boolean (default FALSE). Return a long data.table including a column with the synonyms for each gene. See help for LocToRefSeq for more information.
GeneSymbols	Character vector of gene symbols

Details

Symbols are matched against the OryzabaseGeneListEn database, downloaded from Oryzabase. Rap-DB identifiers from the OryzabaseGeneListEn database are converted to MSU identifiers using the table of RAP-DB and MSU IDs available from Rap-DB. n.b. gene symbols are not necessarily unique so the data.table returned by SearchByGeneSymbol must be manually verified.

Value

Returns a data.frame with MSU IDs as rownames, and columns RapID (RAP-DB gene identifier), symbols (CSGNL recommended symbols) and names (CSGNL recommended names), unless either of shortLabels or return.synonyms is TRUE. See help for LocToRefSeq for more information.

Examples

SearchByGeneSymbol(c('FON1'))
SearchByGeneSymbol(c('SPL7'))

TomHarrop/oryzr documentation built on May 9, 2019, 4:52 p.m.