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Last data update: 2014.03.03

R: Function to compute sliding T statistics on a tiling...

computeSlidingT

R Documentation

Function to compute sliding T statistics on a tiling expression set

Description

Function to compute sliding (regularized) one- or two-sample T statistics on a tiling expression set.

Usage

computeSlidingT(xSet, probeAnno, allChr = c(1:19, "X", "Y"), test = "one.sample", grouping = NULL, winHalfSize = 400, min.probes = 5, checkUnique = TRUE, uniqueCodes = c(0), verbose = TRUE)

Arguments

`xSet`	Object of class `ExpressionSet` holding the normalized probe intensity data
`probeAnno`	Environment holding the genomic positions of probes in the ExpressionSet
`allChr`	Character vector of all chromosomes in genome
`test`	character; one of `one.sample` or `two.sample`
`grouping`	factor vector of length equal to number of samples, not required if `test=one.sample`
`winHalfSize`	Half the size of the window centered at a probe position, in which all other probes contribute to the calculation of the mean and standard deviation.
`min.probes`	integer; if less probes are in the sliding window, NA instead of the mean and sd is returned. This is meant to avoid to computing non-meaningful means and standard deviations. If unwanted, set this to 1 or less
`checkUnique`	logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used.
`uniqueCodes`	numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness?
`verbose`	logical; detailed progress output to STDOUT?

Value

An object of class ExpressionSet, holding the T statistics values for the probes of the supplied ExpressionSet. The number of results samples is the number of levels in the supplied factor grouping.

Author(s)

Joern Toedling

Examples

 exDir <- system.file("exData",package="Ringo")
  load(file.path(exDir,"exampleProbeAnno.rda"))
  load(file.path(exDir,"exampleX.rda"))
  tX <- computeSlidingT(exampleX, probeAnno=exProbeAnno,
             allChr=c("9"), winHalfSize=400)
  sampleNames(tX) <- "t-Stat_Suz12vsTotal"
  if (interactive()){
    grid.newpage()
    plot(cbind2(exampleX, tX), exProbeAnno, chrom="9",
         xlim=c(34318000,34321000), ylim=c(-2,8.5), gff=exGFF,
         paletteName="Paired")
  }

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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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/compute_sliding_t.Rd_%03d_medium.png", width=480, height=480)
> ### Name: computeSlidingT
> ### Title: Function to compute sliding T statistics on a tiling expression
> ###   set
> ### Aliases: computeSlidingT
> ### Keywords: manip
> 
> ### ** Examples
> 
>  exDir <- system.file("exData",package="Ringo")
>   load(file.path(exDir,"exampleProbeAnno.rda"))
>   load(file.path(exDir,"exampleX.rda"))
>   tX <- computeSlidingT(exampleX, probeAnno=exProbeAnno,
+              allChr=c("9"), winHalfSize=400)

 computing probe-wise mean and standard deviation in sliding window.
 chr9  Suz12_vs_total ... 
 computing t-statistics...
preparing result...done.
>   sampleNames(tX) <- "t-Stat_Suz12vsTotal"
> #  if (interactive()){
>     grid.newpage()
>     plot(cbind2(exampleX, tX), exProbeAnno, chrom="9",
+          xlim=c(34318000,34321000), ylim=c(-2,8.5), gff=exGFF,
+          paletteName="Paired")
> #  }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>