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

Source: R/diagnostics.R
PlotMismatchPositionForType.Rd

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

Usage

PlotMismatchPositionForType(
  data,
  genomic,
  read,
  orientation = NULL,
  category = NULL
)

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

Value

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

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).