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.
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
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).