plotSeqOverlap: Plot the quality profile of paired-end data The figure...

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Description

Plot the quality profile of paired-end data The figure created can be used to visually determine the best merging and trimming parameters.

Usage

plotSeqOverlap(
  tabF,
  tabR,
  primerF,
  primerR,
  projectLabel = "Paired-end Study",
  matchScore = 1,
  mismatchScore = -3,
  gapOpeningScore = 5,
  gapExtensionScore = 2,
  minScore = 4
)

Arguments

tabF	(Required). Forward table obtained from the getMeanQualityProfile() function.
tabR	(Required). Reverse table obtained from the getMeanQualityProfile() function.
primerF	(Required). Forward primer sequence provided in the 5' to 3' orientation (must NOT feature any degenerate bases or invalid characters).
primerR	(Required). Reverse primer sequence provided in the 5' to 3' orientation (must NOT feature any degenerate bases or invalid characters).
projectLabel	(Required). Default is "Paired-end Study". Character label (i.e. project accession number) that can be used to describe data being analyzed.
matchScore	(Default is 1). Match alignment score.
mismatchScore	(Default is -3). Mismatch alignment score.
gapOpeningScore	(Default is 5). Gap opening score.
gapExtensionScore	(Default is 2). Gap extension score.
minScore	(Default is 10). Minimum alignment score to accept.

Value

ggplot figure

ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.