| autocor {Ringo} | R Documentation |
Function to compute auto-correlation of probe intensities at specified offsets from the original positions.
autocor(x, probeAnno, chrom = "1", samples = NULL, lag.max = 2000,
lag.step=100, cor.method = "pearson",
channel = c("red","green","logratio"), verbose = TRUE)
x |
an object either of class ExpressionSet containing the
normalized probe intensities or of class RGList containing
the raw intensities. |
probeAnno |
Environment holding chromosomal start positions and indices of probes in data matrix. |
chrom |
character; chromosome to compuute the autocorrelation for |
samples |
which samples of the data to use; if more than 1 for each probe the mean intensity over these samples is taken. |
lag.max |
integer; maximal offset from the original position, the auto-correlation is to be computed for. |
lag.step |
integer; step size of lags between 0 and maximal lag. |
cor.method |
character; which type of correlation to compute,
translates to argument method of function cor |
channel |
character; in case x is an RGList, which
channel to plot, either red, green or the
logratio log2(red)-log2(green) |
verbose |
logical; extended output to STDOUT |
the lags, i.e. the offsets from the original position, the
auto-correlation is to be computed for, are constructed from the
given arguments as seq(0, lag.max, by=lag.step).
Object of class autocor.result, a
numeric vector of auto-correlation values at the offsets specified in
argument lags. The lag values are stored as the names of
the vector. Argument chrom is stored as attribute
chromosome of the result.
Joern Toedling toedling@ebi.ac.uk
exDir <- system.file("exData",package="Ringo")
load(file.path(exDir,"exampleProbeAnno.rda"))
load(file.path(exDir,"exampleX.rda"))
exAc <- autocor(exampleX, probeAnno=exProbeAnno,
chrom="8",lag.step=250)
plot(exAc)