rnaseqcomp-class


This is a S4 class to organize data ready for benchmark summarization.
There are 4 S3 objects inside this class. <code>quantData</code> documents the
data matrix ready for evaluation by functions <code>plotMAD</code>,
<code>plotNE</code> or <code>plotCAT</code>. <code>repInfo</code> is a factor corresponding
to columns of <code>quantData</code> with each level holding 2 elements exactly,
normally the name of quantification methods. <code>refMed</code> is the median
log2 signal of calibration references. <code>scaler</code> is a number that point
to the median log2 signal of reference methods/units, which can be used to
tune the detrended logSignal with 0 corresponding to 1 by reference units.


Several quantitative and visualized benchmarks
for RNA-seq quantification pipelines. Two-replicate
quantifications for genes, transcripts, junctions or
exons by each pipeline with nessasery meta information
should be organizd into numeric matrix in order to
proceed the evaluation.

rnaseqcomp-class: rnaseqcomp

Description

Arguments