## ----ShortRead-fastq-----------------------------------------------------
library(ShortRead)
strm = FastqStreamer("bigdata/SRR1039508_1.fastq.gz", 100000)
fq = yield(strm)
fq
sread(fq)
quality(fq)

## ----r-intro-------------------------------------------------------------
x = rnorm(1000)
y = x + rnorm(1000, sd=.5)
df = data.frame(x=x, y=y)
plot(y ~ x, df)
fit = lm(y ~ x, df)
class(fit)
methods(class=class(fit))
methods("anova")

## ----help, eval=FALSE----------------------------------------------------
## ?log
## ?plot    # generic 'plot'
## ?plot.lm # plot for objects of class 'lm'

## ----S4------------------------------------------------------------------
library(ShortRead)
strm = FastqStreamer("bigdata/SRR1039508_1.fastq.gz", 100000)
fq = yield(strm)          # 'ShortReadQ' S4 class
class(fq)                 # introspection
methods(class=class(fq))  
reads = sread(fq)         # accessor -- get the reads
reads                     # 'DNAStringSet' S4 class
methods(class=class(reads))
gc = letterFrequency(reads, "GC", as.prob=TRUE)
hist(gc)

## ----S4-help, eval=FALSE-------------------------------------------------
## ?DNAStringSet      # class, and often frequently used methods
## ?letterFrequency   # generic
## methods("letterFrequency")
## ?"letterFrequency,XStringSet-method"