boxplot-methods

boxplot,FastqQuality-method

boxplot,SeqExpressionSet-method


High-level functions to produce boxplots of some complex objects.


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

boxplot-methods function

<dl> <dt><code>signature(x = "FastqQuality")</code></dt><dd>
It plots the distribution of the quality per read position.
</dd> <dt><code>signature(x = "SeqExpressionSet")</code></dt><dd>
It plots the distribution of the log counts in each lane of <code>x</code>.
</dd> </dl>

Methods

High-level functions to produce boxplots of some complex objects.

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

Description

Arguments

Methods