createIntUCSCTrack: Annotate genomic ranges

In everettJK/gt23: Gene therapy integration analysis tool suite.

Annotate genomic ranges

Description

Create a dataframe of sequencing run ids associated with 1 or more patient identifiers.

Usage

createIntUCSCTrack(d, abundCuts = c(5, 10, 50),
  posColors = c("#8C9DFF", "#6768E3", "#4234C7", "#1D00AB"),
  negColors = c("#FF8C8C", "#E35D5D", "#C72E2E", "#AB0000"),
  title = "intSites", outputFile = "track.ucsc", visibility = 1,
  position = "chr7:127471196-127495720", padSite = 0, siteLabel = NA)

Arguments

d	Data fram containing genomic ranges to be added to UCSC track.
abundCuts	Cut points for estimated abundance (estAbund) values.
posColors	Color codes for binned abundances (positive integrations).
negColors	Color codes for binned abundances (positive integrations).
title	Track title.
outputFile	Track output file.
visibility	Track default visibility (0 - hide, 1 - dense, 2 - full, 3 - pack, and 4 - squish).
position	Deafult track position.
padSite	Number of NTs to pad sites with for increased visibility.
siteLabel	Text to appear next to sites, ie. 'Patient X, chr12+1052325'.

Value

Nothing.

everettJK/gt23 documentation built on May 16, 2024, 12:04 p.m.