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

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

Description

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

Usage

readSff(filenames, use.qualities=TRUE, use.names=TRUE,
    clipMode = c("full", "adapter", "quality", "raw"), verbose=TRUE)

Arguments

filenames	File or files to be read in.
use.qualities	logical(1) indicating whether to include quality values in the returned object.
use.names	logical(1) indicating whether to return read names, not yet implemented
clipMode	character(1) indicating the clipMode of the returned object.
verbose	logical(1) indicating whether to return verbose output.

Value

A SffReads or SffReadsQ object.

Author(s)

Matt Settles <[e-mail]>

Examples

sff <- readSff(system.file("extdata","Small454Test.sff",package="rSFFreader"))

rSFFreader documentation built on May 6, 2019, 2:02 a.m.