R: Create Genome Browser Track of bidirectional balance scores

trackBalance {CAGEfightR}

R Documentation

Create Genome Browser Track of bidirectional balance scores

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!

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)

[Package CAGEfightR version 1.8.0 Index]