TxFeatures

<code>GRanges</code> with known strand (&#147;+&#148;, &#147;-&#148;)

Character vector or factor, taking value
<code>J</code>, <code>I</code>, <code>F</code>, <code>L</code>, or <code>U</code>

type

<code>CharacterList</code> of transcript names or <code>NULL</code>

txName

<code>CharacterList</code> of gene names or <code>NULL</code>

geneName


Creates an instance of S4 class <code>TxFeatures</code> for storing
transcript features.


SGSeq is a software package for analyzing splice events from
RNA-seq data. Input data are sequence reads mapped to a reference
genome in BAM format. Genes are represented as a genome-wide
splice graph, which can be obtained from existing annotation or
can be predicted from the data. Splice events are identified
from the graph and are quantified locally using structurally
compatible reads at the start or end of each splice variant.
The package includes functions for splice event prediction,
quantification, visualization and interpretation.

TxFeatures: Transcript features

Description

Usage

Arguments

Value

Details

Examples