plotNtFrequency

plotNtFrequency-methods

plotNtFrequency,BamFile-method

plotNtFrequency,ShortRead-method


Plots the nucleotide frequencies per position.


methods

Numerical and graphical summaries of RNA-Seq read data.
Within-lane normalization procedures to adjust for GC-content
effect (or other gene-level effects) on read counts: loess
robust local regression, global-scaling, and full-quantile
normalization (Risso et al., 2011). Between-lane normalization
procedures to adjust for distributional differences between
lanes (e.g., sequencing depth): global-scaling and
full-quantile normalization (Bullard et al., 2010).

Davide Risso

EDASeq

Exploratory Data Analysis and Normalization for RNA-Seq

plotNtFrequency-methods function

<dl> <dt><code>signature(x = "ShortRead")</code></dt><dd>
</dd> <dt><code>signature(x = "BamFile")</code></dt><dd>
</dd> </dl> It plots the nucleotide frequencies per position, averaging all the reads in <code>x</code>. 

Methods

Plots the nucleotide frequencies per position.

plotNtFrequency-methods: Methods for Function `plotNtFrequency` in Package EDASeq

Description

Arguments

Methods