seq_gtf

one of path to GTF file, or data frame representing a canonical
GTF file.

one of path to folder containing one FASTA file (<code>.fa</code>
extension) for each chromosome in <code>gtf</code>, or named DNAStringSet
containing one DNAString per chromosome in <code>gtf</code>, representing its
sequence. In the latter case, <code>names(seqs)</code> should contain the
same entries as the <code>seqnames</code> (first) column of <code>gtf</code>.

seqs

if <code>TRUE</code> (as it is by default), only create transcript
sequences from the features labeled <code>exon</code> in <code>gtf</code>.

exononly

in the <code>attributes</code> column of <code>gtf</code>, what is the
name of the field identifying transcripts? Should be character. Default
<code>"transcript_id"</code>.

idfield

in the <code>attributes</code> column of <code>gtf</code>, how are
attributes separated? Default <code>"; "</code>.

attrsep


Given a GTF file (for transcript structure) and DNA sequences,
  return a DNAStringSet of transcript sequences


This package can be used to simulate RNA-seq reads from
differential expression experiments with replicates. The reads
can then be aligned and used to perform comparisons of methods
for differential expression.

Alyssa Frazee

polyester

Simulate RNA-seq reads

seq_gtf function

Given a GTF file (for transcript structure) and DNA sequences,
  return a DNAStringSet of transcript sequences

seq_gtf: Get transcript sequences from GTF file and sequence info

Description

Usage

Arguments

Value

References

Examples