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## Setting a scale in ggplot2 scale_y_cont …

Setting a scale in ggplot2
scale_y_continuous(limits = c(10, 200))

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## Moving average in R Median: runmed() M …

Moving average in R
Median: runmed()
Mean: filter()

ex)
runmed(data, 3)
filter(data, rep(1/3, 3))

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## Save ggplot in pdf Use dev.copy2pdf(fil …

Save ggplot in pdf
Use dev.copy2pdf(file=”plot.pdf”)

Example)
plotA <- ggplot() + geom_line(data=nucleosome.mono.colsum, aes(seq, y=A, colour="A") ) plotT <- ggplot() + geom_line(data=nucleosome.mono.colsum, aes(seq, y=T, colour="T") ) arranged.plot <- grid.arrange(plotA, plotT, nrow=2) dev.copy2pdf(file="arranged.plot") dev.off()

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## # Running R in batch mode R CMD BATCH R …

# Running R in batch mode
R CMD BATCH Rscript.R

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## Object in R Factor can be used for sequ …

Object in R
Factor can be used for sequence data.

From sequence characters
seq <- c("A", "C", "C", "T", "G") seq.factor <- factor(seq, levels=c("A", "G", "T", "C") From numbers to sequences > seq.num <- c(1,2,3,1,1,3,2,1,4,1,3,2,1) > seq.num.factor <- factor(seq.num, levels=c(1,2,3,4), labels=c("A","G","T","C") )

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## There seems to be a bug in a R package n …

There seems to be a bug in a R package named pgam:periodogram().
The function intensity happened to have two cos. One of them should be sin.
Here is the correct version.

function (w, x)
{
n <- length(x) t <- seq(1:n) sp <- ((sum(x * cos(w * t)))^2 + (sum(x * sin(w * t)))^2)/n return(sp) }

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## R vector does not have dimension. It onl …

R vector does not have dimension. It only has length.
On the other hand, matrix has dimension.

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## R commands to explore time series data …

R commands to explore time series data

ts(data) # create time series objects
time(ts.data) # returns the time

diff(ts.data, lag=1) # difference at the specified lag
lag.plot(ts.data, 9, do.lines=FALSE) # plot with specified lags

plot(stl(ts.data, “per”)) # decomposition of time series data

spec.pgram(ts.data, spans=c(3,3), log=”no”) # non-parametric spectral analysis
spec.ar(ts.data, spans=c(3,3), log=”no”) # parametric estimation

http://www.stat.pitt.edu/stoffer/tsa2/R_time_series_quick_fix.htm

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## R commands examining data and its struct …

R commands examining data and its structures
ls() or objects() # list variables
structure()
str() # summary of data
levels()
dim() # dimension of data
class() # show the class of the variable
head() or tail() # showing parts of data

http://www.statmethods.net/input/contents.html

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## R normality tests shapiro.test() his …

R normality tests

shapiro.test()

hist(data, prob=TRUE)
lines(density(data))

qqnorm(data)
qqline(data)