autocorr: Function to compute auto-correlation of probe intensities
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`x`	an object either of class `ExpressionSet` containing the normalized probe intensities or of class `RGList` containing the raw intensities.
`probeAnno`	Object of class `probeAnno` holding chromosomal match positions and indices of reporters in data matrix.
`chrom`	character; chromosome to compute 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)`
`idColumn`	string; indicating which column of the `genes` data.frame of the `RGList` holds the identifier for reporters on the microarray. Character entries of the `index` elements of the `probeAnno` will be matched against these identifiers. If the `index` elements of the `probeAnno` are numeric or `x` is of class `ExpressionSet`, this argument will be ignored.
`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

cor,plot.autocor.result

  exDir <- system.file("exData",package="Ringo")
  load(file.path(exDir,"exampleProbeAnno.rda"))
  load(file.path(exDir,"exampleX.rda"))
  exAc <- autocor(exampleX, probeAnno=exProbeAnno,
                  chrom="9", lag.max=1000)
  plot(exAc)