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

In kamalfartiyal84/compEpiTools: Tools for computational epigenomics

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)

kamalfartiyal84/compEpiTools documentation built on May 29, 2019, 5:40 a.m.