Load the example 454 dataset

Share:

Description

Load a small, 1000 record example sff file.

Usage

1

Arguments

None

Value

Loads a small example Roche 454 dataset (sff file) into a SffReadsQ object containing 1000 reads.

Author(s)

Matt Settles <msettles@uidaho.edu>

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
##Read in the included sample 454 data set.
sff <- load454SampleData()
##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)