LocToRefSeq: LocToRefSeq

In TomHarrop/oryzr: Work with Oryza sativa gene identifiers

Description

Convert MSU identifiers to Rap-DB identifiers and map them to RefSeq mRNA identifiers. Currently only conversions from MSU ID are implemented.

Usage

LocToRefSeq(LOCs, useBiomart = TRUE)

Arguments

LOCs	Character vector of MSU locus identifiers
useBiomart	Boolean (default TRUE). If biomaRt is installed, use it for secondary searches for genes not matched in the Oryzabase data.

Details

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. Conversion to refSeq mRNA IDs uses the Rice ID IRGSP Build5 database downloaded from Oryzabase. If biomaRt is installed, it can be used for secondary searches for unmatched MSU IDs.

Value

Returns a list of two data.frames, matched for MSU loci that were successfully matched to refSeq IDs and notMatched for ones that weren't. The data.frames each have four columns: tigrId (MSU ID), refseq_mrna (refSeq mRNA ID), ensembl_gene_id (Rap-DB ID) and symbols (CSGNL recommended gene symbol(s)).

Examples

LocToRefSeq(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'))
LocToRefSeq(c('LOC_Os03g03034', 'LOC_Os06g36560', 'LOC_Os01g50910'))

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