distanceFromTSS-methods {compEpiTools} | R Documentation

## 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)

[Package compEpiTools version 1.14.1 Index]