RnaSeqParam class

RnaSeqParam-class

A class holding all the necessary parameters to process a bam file issued
from an RNA-Seq experiment together with the related annotation to compute
a count-table using the <code><a href="/link/simpleRNASeq%20function?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-simpleRNASeq" rd-options="easyRNASeq:easyRNASeq-simpleRNASeq" data-mini-rdoc="easyRNASeq:easyRNASeq-simpleRNASeq::simpleRNASeq function">simpleRNASeq function</a></code>.
The precision slot is used to determine the count unit:
<ul><li>reads</li></ul>{default. The standard <code><a href="/link/GenomicAlignments%20summarizeOverlaps%20function?package=easyRNASeq&version=2.8.2&to=GenomicAlignments%3AsummarizeOverlaps" rd-options="GenomicAlignments:summarizeOverlaps" data-mini-rdoc="GenomicAlignments:summarizeOverlaps::GenomicAlignments summarizeOverlaps function">GenomicAlignments summarizeOverlaps function</a></code> is used to extract the read counts}
<item>bp</item>{The <code><a href="/link/easyRNASeq%20summarization%20functions?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-summarization-methods" rd-options="easyRNASeq:easyRNASeq-summarization-methods" data-mini-rdoc="easyRNASeq:easyRNASeq-summarization-methods::easyRNASeq summarization functions">easyRNASeq summarization functions</a></code> are used to extract the read covered bp counts}

classes

Calculates the coverage of high-throughput short-reads against
    a genome of reference and summarizes it per feature of interest (e.g. exon,
    gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq'
    or 'edgeR' package.

Nicolas Delhomme

easyRNASeq

Count summarization and normalization for RNA-Seq data

RnaSeqParam class function

Objects can be created by calls of the
form <code>new("RnaSeqParam", ...)</code> or using the RnaSeqParam constructor.

Objects from the Class

A class holding all the necessary parameters to process a bam file issued
from an RNA-Seq experiment together with the related annotation to compute
a count-table using the <code><a href="simpleRNASeq function" rd-options="easyRNASeq:easyRNASeq-simpleRNASeq">simpleRNASeq function</a></code>.
The precision slot is used to determine the count unit:
<ul><li>reads</li></ul>{default. The standard <code><a href="GenomicAlignments summarizeOverlaps function" rd-options="GenomicAlignments:summarizeOverlaps">GenomicAlignments summarizeOverlaps function</a></code> is used to extract the read counts}
<item>bp</item>{The <code><a href="easyRNASeq summarization functions" rd-options="easyRNASeq:easyRNASeq-summarization-methods">easyRNASeq summarization functions</a></code> are used to extract the read covered bp counts}

RnaSeqParam class: Class "RnaSeqParam"

Description

Arguments

Objects from the Class

See Also

Examples