trackBalance {CAGEfightR} | R Documentation |
Visualize balance scores used for detectiong of bidirectional sites. Mainly intended as diagnostic tools for expert user.
trackBalance(object, ...) ## S4 method for signature 'GenomicRanges' trackBalance(object, window = 199, plusColor = "cornflowerblue", minusColor = "tomato", balanceColor = "forestgreen", ...) ## S4 method for signature 'RangedSummarizedExperiment' trackBalance(object, ...)
object |
GenomicRanges or RangedSummarizedExperiment: Ranges with CTSSs in the score column. |
... |
additional arguments passed to DataTrack. |
window |
integer: Width of sliding window used for calculating windowed sums. |
plusColor |
character: Color for plus-strand coverage. |
minusColor |
character: Color for minus-strand coverage. |
balanceColor |
character: Color for bidirectional balance. |
list of 3 DataTracks for upstream, downstream and balance.
Potentially consumes a large amount of memory!
Other Genome Browser functions: trackCTSS
,
trackClusters
library(Gviz) data(exampleCTSSs) data(exampleBidirectional) # Calculate pooled CTSSs exampleCTSSs <- calcTPM(exampleCTSSs, totalTags='totalTags') exampleCTSSs <- calcPooled(exampleCTSSs) # Find a bidirectional cluster to plot: BC <- rowRanges(exampleBidirectional[10,]) start(BC) <- start(BC) - 250 end(BC) <- end(BC) + 250 subsetOfCTSSs <- subsetByOverlaps(exampleCTSSs, BC) # Build balance track balance_track <- trackBalance(subsetOfCTSSs) # Plot plotTracks(balance_track, from=start(BC), to=end(BC), chromosome=seqnames(BC))