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)