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Last data update: 2014.03.03

R: Function to compute auto-correlation of probe intensities

autocor

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Ringo)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Ringo/autocorr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: autocor
> ### Title: Function to compute auto-correlation of probe intensities
> ### Aliases: autocorr autocor autocorrelation
> ### Keywords: manip
> 
> ### ** 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)
Lag: 0 ... 100 ... 200 ... 300 ... 400 ... 500 ... 600 ... 700 ... 800 ... 900 ... 1000 ... 
Computing correlation...>   plot(exAc)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>