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

Description Usage Arguments Value See Also Examples

View source: R/hiAnnotator.R

Description

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

Usage

1
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

1
2
3
4
5
6
7
## 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.