compEpiTools (version 1.6.3)

distanceFromTSS-methods: Returns the GRanges annotated with info about the closer TSS

Description

For each GRanges region it decorates the GRanges with extra columns containing info about the closer TSS.

Methods

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.

Examples

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)