tests/test07-complete-channel.R

In PreProcess: Basic Functions for Pre-Processing Microarrays

# complete.channel-test.ssc
library(PreProcess)

suppressWarnings( RNGversion("3.5.3") )
set.seed(989431)
# simulate a complete channel object
v <- rexp(10000, 1/1000)
b <- rnorm(10000, 60, 6)
s <- sapply(v-b, function(x) {max(0, x)})
ct <- ChannelType('user', 'random', 100, 100, 'fake')
x <- CompleteChannel(name='fraud', type=ct,
                      data=data.frame(vol=v, bkgd=b, svol=s))
rm(v, b, s, ct)

summary(x)

opar <- par(mfrow=c(2,3))
plot(x)
plot(x, main='Log Scale', useLog=TRUE)
par(opar)

opar <- par(mfrow=c(2,1))
image(x)
par(opar)

b <- process(x, PROC.NEG.CORRECTED.SIGNAL)
summary(b)

q <- process(b, PIPELINE.STANDARD)
summary(q)

q <- process(x, PIPELINE.MDACC.DEFAULT)
summary(q)

# cleanup
rm(x, b, q, opar)