plotRrnaMappingRate: Plot ribosomal RNA (rRNA) mapping rate

In hbc/bcbioRnaseq: Bcbio RNA-Seq

Plot ribosomal RNA (rRNA) mapping rate

Description

Clean, high-quality samples should have an rRNA mapping rate below 10%. Higher rates are likely indicative of the polyA enrichment or ribo depletion protocol not having removed all ribosomal RNA (rRNA) transcripts. This will reduce the number of biologically meaningful reads in the experiment and is best avoided.

Usage

plotRrnaMappingRate(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotRrnaMappingRate(
  object,
  interestingGroups = NULL,
  limit = 0.1,
  labels = list(title = "rRNA mapping rate", subtitle = NULL, sampleAxis = NULL,
    metricAxis = "rRNA mapping rate (%)"),
  flip = getOption(x = "acid.flip", default = TRUE)
)

Arguments

object	Object.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
limit	numeric(1). Threshold limit.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
flip	logical(1). Flip x and y axes. Recommended for plots containing many samples.
...	Additional arguments.

Value

ggplot.

Note

Updated 2022-05-09.

Author(s)

Michael Steinbaugh, Rory Kirchner, Victor Barrera

Examples

data(bcb)

## bcbioRNASeq ====
plotRrnaMappingRate(bcb)

hbc/bcbioRnaseq documentation built on Sept. 15, 2024, 9:10 a.m.