geneAnnotationPlot: Gene annotation plot

In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Gene annotation plot

Description

Plot read coverage and location of gene annotations that match the keywords and search criteria for contig/chunk currently being assessed

Usage

geneAnnotationPlot(
  geneAnnotSubset,
  keywords,
  pileupSubset,
  colIdx,
  startbpRange,
  endbpRange,
  elevRatio,
  pattern,
  windowSize,
  chunkSize,
  mode
)

Arguments

geneAnnotSubset	Subset of gene annotations to be plotted
keywords	The key-word(s) used for the search.
pileupSubset	A subset of the pileup associated with the contig/chunk being assessed
colIdx	The column index 'gene' or 'product' column
startbpRange	The basepair at which the search is started if a 'specific' search is used
endbpRange	The basepair at which the search is ended if a 'specific' search is used
elevRatio	The maximum/minimum values of the pattern-match
pattern	The pattern-match information associated with the contig/chunk being assessed
windowSize	The number of basepairs to average read coverage values over.

ProActive documentation built on April 4, 2025, 12:58 a.m.