trackBalance: Create Genome Browser Track of bidirectional balance scores

Description Usage Arguments Value Note See Also Examples

Description

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

Usage

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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

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## 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)

MalteThodberg/CAGEfightR documentation built on Oct. 24, 2018, 12:10 p.m.