autocor {Ringo}R Documentation

Function to compute auto-correlation of probe intensities

Description

Function to compute auto-correlation of probe intensities at specified offsets from the original positions.

Usage

autocor(x, probeAnno, chrom = "1", samples = NULL, lag.max = 2000,
lag.step=100, cor.method = "pearson", 
channel = c("red","green","logratio"), verbose = TRUE)

Arguments

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

Details

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).

Value

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.

Author(s)

Joern Toedling toedling@ebi.ac.uk

See Also

cor,plot.autocor.result

Examples

  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)

[Package Ringo version 1.0.0 Index]