getUCSCtable: Obtain a UCSC annotation table given the table & track name.

In malnirav/hiAnnotator: Functions for annotating GRanges objects

Description

Obtain a UCSC annotation table given the table & track name.

Usage

getUCSCtable(tableName, trackName, bsession = NULL, freeze = "hg19", ...)

Arguments

tableName	Name of the annotation table as it appears on UCSC browser.
trackName	Name of the track annotation table as it appears in on UCSC browser.
bsession	UCSC session object returned by makeUCSCsession or browserSession. If left NULL the function will call makeUCSCsession with the provided freeze to initiate a session.
freeze	one of following: hg19, mm8, rheM, etc. Default is hg19.
...	Arguments to be passed to ucscTableQuery.

Value

a dataframe containing the annotation data.

See Also

makeUCSCsession, getNearestFeature, getSitesInFeature.

Examples

## Not run: 
refflat <- getUCSCtable("refFlat", "RefSeq Genes")
## same as above ##
refflat <- getUCSCtable("refFlat", "RefSeq Genes",
bsession=session,freeze="hg19")

## End(Not run)

malnirav/hiAnnotator documentation built on July 29, 2021, 6:32 a.m.