makeTrack {iGenomicViewer}R Documentation

Creates a trackRegion object

Description

This function creates a track region object. This object is utilized in makeGGV to store known genomic regions of interest.

Usage


makeTrack(Broad.Band=NA,
          Fine.Band=NA,
          genomicLoc=NA,
          geneName=NA)

Arguments

Broad.Band character vector of broad band regions. These regions should match to an associated mapObj$band.info$Broad.Band
Fine.Band character vector of fine band regions. These regions should match to an associated mapObj$band.info$Fine.Band
genomicLoc numeric vector or matrix of genomic locations. see details
geneName character vector of geneNames, or name in label column of an associated annObj's annotation data.frame.

Details

The makeTrack function makes a trackRegion object to store known regions of interest. There are four ways to speicify a region: broad band, fine band, genomic start and stop locations, and geneName.

Broad.Band and Fine.Band are character vectors containing names of broad band or fine band regions. They should match an entry in the broad.band or fine.band column in a mapObj$band.info data frames object. The geneName character vector is associates with an annObj. This character vector should contain entries that match the labels in the columns of an annObj's annotation data.frame. The list may contain entries from any and all objects of the annObj. The genomicLoc entry may either be a numeric vector or matrix. If it is a vector it assumes the entries are listed in order of start loc, stop loc, start loc, stop loc, for given regions. If it is a matrix, it assumes the first column is start locations and the second is stop locations.

Any of the four entries may be left as NA.

A trackRegion object is returned. This object is a list of known regions, with entries for Broad.Band, Fine.Band, genomicLoc, and geneName.

Value

trackRegion object, list containing known regions of interest, see details

Note

see vignette for more details

Author(s)

Lori A. Shepherd

See Also

updateGGV, makeGGV

Examples


library("iGenomicViewer")

trackRegion = makeTrack(Fine.Band = c("8p11.22","18p11.21"),
                        genomicLoc = NA,
                        geneName = "FANCE")


[Package iGenomicViewer version 2.4.6 Index]