plot5Prime3PrimeBias: Plot 5' to 3' bias

In steinbaugh/bioverbs: Acid Genomics Generics

Plot 5' to 3' bias

Description

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

Usage

plot5Prime3PrimeBias(object, ...)

Arguments

object	Object.
...	Additional arguments.

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.

Value

ggplot.

Examples

showMethods("plot5Prime3PrimeBias")

steinbaugh/bioverbs documentation built on April 10, 2024, 7:21 a.m.