Read SFF-formatted files into SffReads or SffReadsQ objects

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

Value

A SffReads or SffReadsQ object.

Author(s)

Matt Settles <msettles@uidaho.edu>

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(rSFFreader)
Loading required package: ShortRead
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rSFFreader/readsff.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readSff
> ### Title: Read SFF-formatted files into SffReads or SffReadsQ objects
> ### Aliases: readSff
> 
> ### ** Examples
> 
> sff <- readSff(system.file("extdata","Small454Test.sff",package="rSFFreader"))
Total number of reads to be read: 1000
reading header for sff file:/home/ddbj/local/lib64/R/library/rSFFreader/extdata/Small454Test.sff
reading file:/home/ddbj/local/lib64/R/library/rSFFreader/extdata/Small454Test.sff
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>