QuantitativeTrack-class: Constructor for QuantitativeTrack

In PriceLab/igvR: igvR: integrative genomics viewer

Constructor for QuantitativeTrack

Description

QuantitativeTrack creates an IGV track for genomic tracks in which a numerical value is associated with each reported location.

Usage

QuantitativeTrack(
  trackName,
  quantitativeData,
  fileFormat = c("wig", "bigWig", "bedGraph"),
  color = "gray",
  sourceType = "file",
  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 polyvalent object, either a data.frame, GRanges, or UCSCBedGraphQuantitative object
fileFormat	only "bedGraph" supported at present; wig and bigWig support soon.
color	A CSS color name (e.g., "red" or "#FF0000")
sourceType	only "file" supported at present ("gcs" for Google Cloud Storage, and "ga4gh" for the Global Alliance API may come)
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 will go here

Value

A QuantitativeTrack object

PriceLab/igvR documentation built on Sept. 6, 2022, 5:45 a.m.