GRangesQuantitativeTrack-class: Constructor for GRangesQuantitativeTrack

Description Usage Arguments Details Value Examples

Description

GRangesQuantitativeTrack creates and IGV track for bed objects imported using rtracklayer

Usage

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GRangesQuantitativeTrack(trackName, quantitativeData, color = "blue",
  trackHeight = 50, autoscale = TRUE, min = NA_real_,
  max = NA_real_, visibilityWindow = 1e+05)

Arguments

trackName

A character string, used as track label by igv, we recommend unique names per track.

quantitativeData

A GRanges object with (at least) a "score" metadata column

color

A CSS color name (e.g., "red" or "#FF0000")

trackHeight

track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)

autoscale

Autoscale track to maximum value in view

min

Sets the minimum value for the data (y-axis) scale. Usually zero.

max

Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE

visibilityWindow

Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.

Details

Detailed description goes here

Value

A GRangesQuantitativeTrack object

Examples

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base.loc <- 88883100
tbl <- data.frame(chrom=rep("chr5", 3),
                  start=c(base.loc, base.loc+100, base.loc + 250),
                  end=c(base.loc + 50, base.loc+120, base.loc+290),
                  name=c("a", "b", "c"),
                  score=runif(3),
                  strand=rep("*", 3),
                  stringsAsFactors=FALSE)

gr <- GRanges(tbl)
track <- GRangesQuantitativeTrack("GRangesQTest", gr)

paul-shannon/IGV documentation built on Sept. 30, 2018, 1:04 p.m.