importTranscripts

Character string specifying input GFF file

file

GFF attribute tag for transcript identifier

tag_tx

tag_gene

Import GFF file and generate a <code>GRangesList</code> of transcripts
suitable as input for functions <code>convertToTxFeatures</code> or
<code>predictVariantEffects</code>.

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.

importTranscripts: Import transcripts from GFF file

Description

Usage

Arguments

Value

Examples