trackBalance: Create Genome Browser Track of bidirectional balance scores

In CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

Visualize balance scores used for detectiong of bidirectional sites. Mainly intended as diagnostic tools for expert user.

Usage

trackBalance(object, ...)

## S4 method for signature 'GRanges'
trackBalance(
  object,
  window = 199,
  plusColor = "cornflowerblue",
  minusColor = "tomato",
  balanceColor = "forestgreen",
  ...
)

## S4 method for signature 'GPos'
trackBalance(object, ...)

## S4 method for signature 'RangedSummarizedExperiment'
trackBalance(object, ...)

Arguments

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.

Value

list of 3 DataTracks for upstream, downstream and balance.

Note

Potentially consumes a large amount of memory!

See Also

Other Genome Browser functions: trackCTSS(), trackClusters(), trackLinks()

Examples

## Not run: 
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))

## End(Not run)

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.