various kernel functions for computations in MACAT

Description

Various Kernel functions for computations in MACAT. Normally not called by user. All kernel functions have the same arguments in the same order!!!

Usage

kNN(geneLocations, position, params)
rbf(geneLocations, position, params = list(gamma=1/10^13))
basePairDistance(geneLocations, position, params = list(distance = 1e+06))

Arguments

Details

For internal use by other MACAT-functions. Not called by user.

Value

returns kernel weight for position, computed from the geneLocations

Author(s)

MACAT development team

See Also

evalScoring, compute.sliding, kernelize

Examples

  data(stjd)
  genes = seq(100)
  geneLocations = abs(stjd$geneLocation[genes])
  position = c(1000) # location for which you want the kernelweights
  kernelweights = rbf(as.matrix(geneLocations), as.matrix(position), 
  		      list(gamma=1/10e13))
  hist(kernelweights)  

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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/kernels.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Kernels
> ### Title: various kernel functions for computations in MACAT
> ### Aliases: kNN rbf basePairDistance fitkernelparams kernels
> ### Keywords: internal
> 
> ### ** Examples
> 
>   data(stjd)
>   genes = seq(100)
>   geneLocations = abs(stjd$geneLocation[genes])
>   position = c(1000) # location for which you want the kernelweights
>   kernelweights = rbf(as.matrix(geneLocations), as.matrix(position), 
+   		      list(gamma=1/10e13))
>   hist(kernelweights)  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>