plot-methods

plot,BamFileList,FastqFileList-method


High-level function to produce plots given one <code>BamFileList</code> object and one <code>FastqFileList</code> object.


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

plot-methods function

<dl> <dt><code>signature(x = "BamFileList", y = "FastqFileList")</code></dt><dd>
It produce a barplot of the percentage of mapped reads. If <code>strata=TRUE</code> it stratifies the bars according to the unique/non-unique mapped reads.
To be meaningful, <code>x</code> should be a set of aligned reads and <code>y</code> a set of raw reads on the same samples.
</dd> </dl>

Methods

High-level function to produce plots given one <code>BamFileList</code> object and one <code>FastqFileList</code> object.

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

Description

Arguments

Methods