SangerRead-class-generateReportSR: generateReportSR

In roblanf/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

generateReportSR

Description

A SangerRead method which generates final reports of the SangerRead instance.

Usage

## S4 method for signature 'SangerRead'
generateReportSR(
  object,
  outputDir,
  colors,
  navigationContigFN = NULL,
  navigationAlignmentFN = NULL
)

Arguments

object	A SangerRead S4 instance.
outputDir	The output directory of the generated HTML report.
colors	A vector for users to set the colors of (A, T, C, G, else). There are three options for users to choose from. 1. "default": (green, blue, black, red, purple). 2. "cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121, 167)). 3. Users can set their own colors with a vector with five elements.
navigationContigFN	The internal parameter passed to HTML report. Users should not modify this parameter on their own.
navigationAlignmentFN	The internal parameter passed to HTML report. Users should not modify this parameter on their own.

Value

The output absolute path to the SangerRead's HTML file.

Examples

data("sangerReadFData")
## Not run: 
generateReportSR(sangerReadFData, "~/Documents")
generateReportSR(sangerReadFData, colors="cb_friendly")
## End(Not run)

roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.