readSff

filenames

<code>logical(1)</code> indicating whether to include quality values in the returned object.

use.qualities

<code>logical(1)</code> indicating whether to return read names, not yet implemented

use.names

<code>character(1)</code> indicating the clipMode of the returned object.

clipMode

<code>logical(1)</code> indicating whether to return verbose output.

verbose


  <code>readSff</code> reads all sff files specified in <code>filenames</code>, returning an R object of type <code>SffReads</code> or 
  <code>SffReadsQ</code> which acts and behaves similarly to the <code>ShortRead</code> and <code>ShortReadQ</code> 
  classes from package ShortRead


rSFFreader reads sequence, qualities and clip point values
from sff files generated by Roche 454 and Life Sciences Ion
Torrent sequencers into similar classes as are present for fastq files.

Matt Settles

rSFFreader

rSFFreader reads in sff files generated by Roche 454 and Life
Sciences Ion Torrent sequencers

readSff function

<code>readSff</code> reads all sff files specified in <code>filenames</code>, returning an R object of type <code><linkS4class>SffReads</linkS4class></code> or 
  <code><linkS4class>SffReadsQ</linkS4class></code> which acts and behaves similarly to the <code><linkS4class>ShortRead</linkS4class></code> and <code><linkS4class>ShortReadQ</linkS4class></code> 
  classes from package ShortRead

readSff: Read SFF-formatted files into SffReads or SffReadsQ objects

Description

Usage

Arguments

Value

Examples