Plot 5' to 3' bias

RNA-seq data can have specific biases at either the 5’ or 3’ end of sequenced fragments.

plot5Prime3PrimeBias(object, ...)

# S4 method for bcbioRNASeq
plot5Prime3PrimeBias(object,
  interestingGroups = NULL, color = getOption(x =
  "acid.color.discrete", default = acidplots::scale_color_synesthesia_d()),
  labels = list(title = "5'->3' bias", subtitle = NULL, sampleAxis =
  NULL, metricAxis = "5'->3' bias"), 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.
color	ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual(). To set the discrete color palette globally, use: options(acid.color.discrete = ggplot2::scale_color_viridis_d())
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.

Details

It is common to see a small amount of bias, especially if polyA enrichment was performed, or if there is any sample degradation. If a large amount of bias is observed here, be sure to analyze the samples with a Bioanalyzer and check the RIN scores.

5' (3') bias is generally calculated as the median of the following ratio:

[mean expression of 5' (3')] /
    [mean expression of whole transcript]

For example:

• Mean expression for 5' (3') is calculated as mean coverage of first (last) 100 bases.

• Mean expression of transcript is the mean coverage of all bases in that transcript.

• Median is calculated for the representative set of 1000 transcripts.

Note

Updated 2019-09-16.

Examples

data(bcb)
plot5Prime3PrimeBias(bcb)