barplot-methods

barplot,BamFile-method

barplot,BamFileList-method

barplot,FastqFileList-method


High-level functions to produce barplots 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

barplot-methods function

<dl> <dt><code>signature(height = "BamFile")</code></dt><dd>
Usage: barplot(height,strata=c("rname","strand"))
It produces a barplot of the total number of reads in each chromosome (if "rname") or strand.
</dd> <dt><code>signature(height = "BamFileList")</code></dt><dd>
It produces a barplot of the total number of reads in each object in <code>height</code>. If <code>unique=TRUE</code> is specified, it stratified the total by uniquely/non-uniquely mapped reads.
</dd> <dt><code>signature(height = "FastqFileList")</code></dt><dd>
It produces a barplot of the total number of reads in each object in <code>height</code>.
</dd> </dl>

Methods

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

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

Description

Arguments

Methods