R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Discretize and smooth expression values

discreteKernelize

R Documentation

Discretize and smooth expression values

Description

returns discretized kernelized expression values and saves them to a file if argument 'saveToFile' is TRUE. For details on discretization see discretize.

Usage

discreteKernelize(data, chrom, margin = 10, step.width = 1e+05, kernel = rbf,
                  kernelparams = list(gamma = 1/10^13), saveToFile = FALSE)

Arguments

`data`	MACATData Object
`chrom`	chromosome to kernelize
`margin`	symmetric qunatile in percent
`step.width`	size of the interpolation steps
`kernel`	kernel function one of rbf, kNN, basePairDistance or your own
`kernelparams`	list of named kernel parameters
`saveToFile`	logicval indicating whether to write a flatfile or not; default is FALSE

Details

Filename of the flatfile is: discrete_kernelized_seq_margin_<margin>_chrom_<chrom>.py where <margin> is the discretization parameter and <chrom> the name of the chromosome.

Value

discretized and kernelized expression matrix

Author(s)

The MACAT Development team

Examples

   #loaddatapkg("stjudem")
   #data(stjude)
   data(stjd)
   discretizedKernelized = discreteKernelize(stjd, 13)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(macat)
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: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading MicroArray Chromosome Analysis Tool...
Loading required packages...

Type 'demo(macatdemo)' for a quick tour...

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/macat/discreteKernelize.Rd_%03d_medium.png", width=480, height=480)
> ### Name: discreteKernelize
> ### Title: Discretize and smooth expression values
> ### Aliases: discreteKernelize
> ### Keywords: manip
> 
> ### ** Examples
> 
>    #loaddatapkg("stjudem")
>    #data(stjude)
>    data(stjd)
>    discretizedKernelized = discreteKernelize(stjd, 13)
Computing kernel weights
Kernelizing
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>