Load the example Ion Torrent dataset

Description

Load a small, 1000 record example sff file.

Usage

load454SampleData()

Arguments

None

Value

Loads a small example Life Sciences Ion Torrent dataset (sff file) into a SffReadsQ object containing 1000 reads.

Author(s)

Matt Settles <msettles@uidaho.edu>

Examples

##Read in the included Ion Torrent sample data set.
sff <- loadIonSampleData()
##Generate summary statistics for read lengths.
summary(width(sff))

##Generate some QA plots:
##Read length histograms:
par(mfrow=c(2,2))
clipMode(sff) <- "raw"
hist(width(sff),breaks=500,col="grey",xlab="Read Length",main="Raw Read Length")

clipMode(sff) <- "full"
hist(width(sff),breaks=500,col="grey",xlab="Read Length",main="Clipped Read Length")

## Base by position plots:
clipMode(sff) <- "raw"
ac <- alphabetByCycle(sread(sff),alphabet=c("A","C","T","G","N"))
ac.reads <- apply(ac,2,sum)
acf <- sweep(ac,MARGIN=2,FUN="/",STATS=apply(ac,2,sum))

matplot(cbind(t(acf),ac.reads/ac.reads[1]),col=c("green","blue","black","red","darkgrey","purple"),
          type="l",lty=1,xlab="Base Position",ylab="Base Frequency",
          main="Base by position")
cols <- c("green","blue","black","red","darkgrey","purple")
leg <-  c("A","C","T","G","N","%reads")
legend("topright", col=cols, legend=leg, pch=18, cex=.8)

clipMode(sff) <- "full"
ac <- alphabetByCycle(sread(sff),alphabet=c("A","C","T","G","N"))
ac.reads <- apply(ac,2,sum)
acf <- sweep(ac,MARGIN=2,FUN="/",STATS=apply(ac,2,sum))

matplot(cbind(t(acf),ac.reads/ac.reads[1]),col=c("green","blue","black","red","darkgrey","purple"),
          type="l",lty=1,xlab="Base Position",ylab="Base Frequency",
          main="Base by position")
legend("topright", col=cols, legend=leg, pch=18, cex=.8)

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)

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> 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/loadIonSampleData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: loadIonSampleData
> ### Title: Load the example Ion Torrent dataset
> ### Aliases: loadIonSampleData
> 
> ### ** Examples
> 
> ##Read in the included Ion Torrent sample data set.
> sff <- loadIonSampleData()
Total number of reads to be read: 1000
reading header for sff file:/home/ddbj/local/lib64/R/library/rSFFreader/extdata/SmallTorrentTest.sff
reading file:/home/ddbj/local/lib64/R/library/rSFFreader/extdata/SmallTorrentTest.sff
> ##Generate summary statistics for read lengths.
> summary(width(sff))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    5.0   140.0   266.0   215.3   297.0   353.0 
> 
> ##Generate some QA plots:
> ##Read length histograms:
> par(mfrow=c(2,2))
> clipMode(sff) <- "raw"
> hist(width(sff),breaks=500,col="grey",xlab="Read Length",main="Raw Read Length")
> 
> clipMode(sff) <- "full"
> hist(width(sff),breaks=500,col="grey",xlab="Read Length",main="Clipped Read Length")
> 
> ## Base by position plots:
> clipMode(sff) <- "raw"
> ac <- alphabetByCycle(sread(sff),alphabet=c("A","C","T","G","N"))
> ac.reads <- apply(ac,2,sum)
> acf <- sweep(ac,MARGIN=2,FUN="/",STATS=apply(ac,2,sum))
> 
> matplot(cbind(t(acf),ac.reads/ac.reads[1]),col=c("green","blue","black","red","darkgrey","purple"),
+           type="l",lty=1,xlab="Base Position",ylab="Base Frequency",
+           main="Base by position")
> cols <- c("green","blue","black","red","darkgrey","purple")
> leg <-  c("A","C","T","G","N","%reads")
> legend("topright", col=cols, legend=leg, pch=18, cex=.8)
> 
> clipMode(sff) <- "full"
> ac <- alphabetByCycle(sread(sff),alphabet=c("A","C","T","G","N"))
> ac.reads <- apply(ac,2,sum)
> acf <- sweep(ac,MARGIN=2,FUN="/",STATS=apply(ac,2,sum))
> 
> matplot(cbind(t(acf),ac.reads/ac.reads[1]),col=c("green","blue","black","red","darkgrey","purple"),
+           type="l",lty=1,xlab="Base Position",ylab="Base Frequency",
+           main="Base by position")
> legend("topright", col=cols, legend=leg, pch=18, cex=.8)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>