distanceFromTSS-methods {compEpiTools} | R Documentation |
For each GRanges region it decorates the GRanges with extra columns containing info about the closer TSS.
To be used in this form:
distanceFromTSS(Object, txdb, EG2GS=NULL)
where:
Object: GRanges
txdb: TxDb
EG2GS: an object of class OrgDb; like org.Mm.eg.db, org.Hs.eg.db (use the exact name of object)
The method returns a GRanges with additional columns. If EG2GS is NULL three columns are appended containing info for the gene with the closer TSS:
nearest_tx_name: the transcript id
distance_fromTSS: the distance in bp
nearest_gene_id: gene id
If EG2GS is provided, gene symbols are also included as additional column.
require(TxDb.Mmusculus.UCSC.mm9.knownGene) txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene isActiveSeq(txdb) <- c(TRUE, rep(FALSE, length(isActiveSeq(txdb))-1)) TSSpos <- TSS(txdb) gr <- TSSpos[1:5] start(gr) <- start(gr)-1000 end(gr) <- end(gr)-600 mcols(gr) <- NULL distanceFromTSS(Object=gr, txdb=txdb, EG2GS=NULL) restoreSeqlevels(txdb)