.geneModelAnnotation

.getBmRange

.getGffRange

.getGtfRange

.readGffGtf

easyRNASeq annotation internal methods

an <code><links4class>AnnotParam</links4class></code> object containing the
necessary retrieval information (datasource and type)

Additional arguments, passed to more internal functions.

describes the kind of annotation to keep the
information from in a gtf or gff file. If set to NULL all the annotations
are returned.

annotation.type

added a parameter that allows defining the fields parsed from
a gtf file. Still internal, but could easily be externalized.

fields

filename

describes the kind of annotation provided. One of gtf or gff.

format

a <code><links4class>RangedData</links4class></code> object containing exon
annotations

gAnnot

nbCore

These are internal methods used to retrieve annotations tabularll
<code>.getBmRange</code>Use <code><a href="/link/biomaRt?package=easyRNASeq&version=2.8.2&to=biomaRt%3AuseMart" rd-options="biomaRt:useMart" data-mini-rdoc="biomaRt:useMart::biomaRt">biomaRt</a></code> to get exon
annotations.  <code>.getGffRange</code>Use
<code><links4class>Genome_intervals_stranded</links4class></code> to get annotation from a gff
file.  <code>.getGtfRange</code>Use
<code><links4class>Genome_intervals_stranded</links4class></code> to get annotation from a gtf
file.  <code>.geneModelAnnotation</code>Use the provided exon annotation to
define gene models.  <code>.readGffGtf</code>Use
<code><links4class>Genome_intervals_stranded</links4class></code> to get annotation from a gff
or gtf file. It is called from <code>getGffRange</code> and <code>getGtfRange</code>.

internal

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

easyRNASeq annotation internal methods function

an <code><linkS4class>AnnotParam</linkS4class></code> object containing the
necessary retrieval information (datasource and type)

a <code><linkS4class>RangedData</linkS4class></code> object containing exon
annotations

These are internal methods used to retrieve annotations tabularll
<code>.getBmRange</code>Use <code><a href="biomaRt" rd-options="biomaRt:useMart">biomaRt</a></code> to get exon
annotations.  <code>.getGffRange</code>Use
<code><linkS4class>Genome_intervals_stranded</linkS4class></code> to get annotation from a gff
file.  <code>.getGtfRange</code>Use
<code><linkS4class>Genome_intervals_stranded</linkS4class></code> to get annotation from a gtf
file.  <code>.geneModelAnnotation</code>Use the provided exon annotation to
define gene models.  <code>.readGffGtf</code>Use
<code><linkS4class>Genome_intervals_stranded</linkS4class></code> to get annotation from a gff
or gtf file. It is called from <code>getGffRange</code> and <code>getGtfRange</code>.

easyRNASeq annotation internal methods: Internal easyRNASeq annotation methods

Description

Usage

Arguments

Value

Details