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

### Arguments

`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

### 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

### 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="9", lag.max=1000)
      plot(exAc)

[Package Ringo version 1.42.1 Index]