updateGGV {iGenomicViewer}R Documentation

Updates a 'GGV' object with new known track regions

Description

This fucntion will update a GGV object with new known regions of interest.

Usage

updateGGV(GGV,
          trackRegions,
          appendTo=TRUE,
          returnVl=TRUE,
          saveFlag=FALSE,
          saveName="GGVobj.RData")

Arguments

GGV A GGV object. See initGGV
trackRegions A object made by or with the same structure as the makeTrack function. See makeTrack
appendTo Logical indicating if the regions should be added to the existing trackRegion object or if the new regions should totally replace the GGV object trackRegions
returnVl Should GGV object be returned
saveFlag Should GGV object be saved
saveName If saveFlag, path file name to save object

Details

This function acts on an exisiting GGV object. The user can either replace the known regions in the GGV with new regions, or append new regions to the existing GGV trackRegion object.

For more information on trackRegion see makeTrack help file or package vignette.

Value

If returnVl, a new updated GGV object is returned.

Note

see vignette for more details

Author(s)

Lori A. Shepherd

See Also

initGGV, makeTrack, GGVobj

Examples


# load library
library("iGenomicViewer")

# load example data
data(iGGVex)
data(mapping.info)
data(annObj)

mapObj = mapping.info
chrArm = c("8p", "18p")
y.lbls$Pdisc = round(y.lbls$Pdisc,3)
pvls = rep(rep(rep(1:4, each=5), 960))[1:length(mapObj$mapping.info$g.loc.center)]
plot.vec = pvls[1:length(mapObj$mapping.info$g.loc.center)]
side.plot.extras="title(main='pvals'"

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

# make GGV object
GGV = initGGV(vls = round(mat, 3),
              mapObj = mapObj,
              annObj = annObj,
              x.labels=x.lbls,
              y.labels=y.lbls,
              xy.labels=NA,
              chrArms=chrArm,
              trackRegions=trackRegion,
              side.plot.extras=side.plot.extras,
              plot.vec=plot.vec,
              plot.dx=which(mapObj$mapping.info$Chrom=="chr8"),
              mapObj.columns =c(2,8,10),
              smpLines=TRUE,
              divCol="lightgrey")

# make new track region
trackRegionUpdate = makeTrack(geneName="MYC")

# this will append new regions to old object regions
GGVnew = updateGGV(GGV=GGV,
                   trackRegions=trackRegionUpdate,
                   appendTo=TRUE)


# this will replace GGV object's trackregions with
# new object
GGVnew = updateGGV(GGV=GGV,
                   trackRegions=trackRegionUpdate,
                   appendTo=FALSE)



[Package iGenomicViewer version 2.4.6 Index]