PlotMismatchPositionForType: Diagnostic plot for mismatch position for columns (by...

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Diagnostic plot for mismatch position for columns (by mismatch type)

Description

This belongs to the first diagnostic plots (raw mismatches) generated by GRAND3.

Usage

PlotMismatchPositionForType(
  data,
  genomic,
  read,
  orientation = NULL,
  category = NULL,
  max.pos = 2500
)

Arguments

data	a grandR object
genomic	the nucleotide as it occurs in the genome
read	the nucleotide as it occurs in the read
orientation	restrict to either Sense or Antisense; can be NULL
category	restrict to a specific category (see GetDiagnosticParameters); can be NULL
max.pos	remove everything behind this position

Details

For all positions along the reads (x axis; potentially paired end, shown left and right), show the percentage of a specific mismatch type for all samples. Positions outside of shaded areas are clipped. Uncorrected and Retained means before and after correcting multiply sequenced bases. Sense/Antisense means reads (first read for paired end) that are (based on the annotation) oriented in sense or antisense direction to a gene (i.e. this is only relevant for sequencing protocols that do not preserve strand information).

Value

a list with a ggplot object, a description, and the desired size for the plot

grandR documentation built on April 4, 2025, 2:27 a.m.