Deprecated functions

easyRNASeq

easyRNASeq,RNAseq-method

fetchCoverage

fetchCoverage,RNAseq-method

<ul><li>The<code><a href="/link/easyRNASeq?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-easyRNASeq" rd-options="easyRNASeq:easyRNASeq-easyRNASeq" data-mini-rdoc="easyRNASeq:easyRNASeq-easyRNASeq::easyRNASeq">easyRNASeq</a></code>function is superseded by the<code><a href="/link/simpleRNASeq?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-simpleRNASeq" rd-options="easyRNASeq:easyRNASeq-simpleRNASeq" data-mini-rdoc="easyRNASeq:easyRNASeq-simpleRNASeq::simpleRNASeq">simpleRNASeq</a></code>function to consolidate and
prune the overall package. The changes are based on user comments and on the
general standardization occuring in the field.</li><li>The<code><a href="/link/fetchCoverage?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-coverage-methods" rd-options="easyRNASeq:easyRNASeq-coverage-methods" data-mini-rdoc="easyRNASeq:easyRNASeq-coverage-methods::fetchCoverage">fetchCoverage</a></code>function only had two
parameters deprecated as the consequence of the package consolidation. As the scanBam
function is not called directly anymore but through higher level functions (from the
GenomicRanges package), the 'what' and 'isUnmappedQuery' parameters were obsolete.</li></ul>

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

Count summarization and normalization for RNA-Seq data

Deprecated functions function

<ul><li>The<code><a href="easyRNASeq" rd-options="easyRNASeq:easyRNASeq-easyRNASeq">easyRNASeq</a></code>function is superseded by the<code><a href="simpleRNASeq" rd-options="easyRNASeq:easyRNASeq-simpleRNASeq">simpleRNASeq</a></code>function to consolidate and
prune the overall package. The changes are based on user comments and on the
general standardization occuring in the field.</li><li>The<code><a href="fetchCoverage" rd-options="easyRNASeq:easyRNASeq-coverage-methods">fetchCoverage</a></code>function only had two
parameters deprecated as the consequence of the package consolidation. As the scanBam
function is not called directly anymore but through higher level functions (from the
GenomicRanges package), the 'what' and 'isUnmappedQuery' parameters were obsolete.</li></ul>

The following function have been deprecated:
<ul><li><code><a href="easyRNASeq" rd-options="easyRNASeq:easyRNASeq-easyRNASeq">easyRNASeq</a></code></li><li><code><a href="fetchCoverage" rd-options="easyRNASeq:easyRNASeq-coverage-methods">fetchCoverage</a></code></li></ul>

The following function have been deprecated:
<ul><li><code><a href="/link/easyRNASeq?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-easyRNASeq" rd-options="easyRNASeq:easyRNASeq-easyRNASeq" data-mini-rdoc="easyRNASeq:easyRNASeq-easyRNASeq::easyRNASeq">easyRNASeq</a></code></li><li><code><a href="/link/fetchCoverage?package=easyRNASeq&version=2.8.2&to=easyRNASeq%3AeasyRNASeq-coverage-methods" rd-options="easyRNASeq:easyRNASeq-coverage-methods" data-mini-rdoc="easyRNASeq:easyRNASeq-coverage-methods::fetchCoverage">fetchCoverage</a></code></li></ul>

Deprecated functions: The following function have been deprecated:
`easyRNASeq`
`fetchCoverage`

Description

Arguments