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Last data update: 2014.03.03

R: Classify two Binding Profiles - Increased Binding

increasedBindingRegions

R Documentation

Classify two Binding Profiles - Increased Binding

Description

This function is used to classify two Binding Profiles into regions which are more bound in one data set than the other.

Usage

increasedBindingRegions(xSet, sgrset = c(1, 2), bound.cutoff, diff.cutoff, probes, 
  probe.max.spacing, writeBedFile = TRUE)

Arguments

`xSet`	object of class ExpressionSet
`sgrset`	vector of lenght 2; specifying which data sets to compare from the ExpressionSet
`bound.cutoff`	numeric; threshold above probes are considered “bound”
`diff.cutoff`	numeric; difference threshold to determine if object 1 and object 2 are uniquely bound
`probes`	integer; minimum number of probes in a valid region
`probe.max.spacing`	integer; maximum number of base pairs in a gap before splitting a region into 2 regions
`writeBedFile`	logical; should a bed file be written

Details

Probe signal values above the bound.cutoff threshold for both data sets are compared where set 1 is above the diff.cutoff of set 2. These probes are then filtered into regions using the probes and probe.max.spacing details. The score is calculated as mean (probes in region set 1 minus set 2). Optional bed file formated result files are written using the choosen options in the file names.

Value

data.frame with the following columns:

`name`	name(s) of data set to which region belongs
`class.group`	class group, in this case only 1
`chr`	chromsome
`start`	start position of region
`end`	end position of region
`scrore`	score of region
`nProbes`	number of probes in region

Author(s)

Bettina Fischer, Robert Stojnic

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  overcompBC <- increasedBindingRegions(SGR, sgrset=c(2,3), bound.cutoff=1.86, diff.cutoff=1.4, 
                probes=10, probe.max.spacing=200)

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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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(SimBindProfiles)
Loading required package: 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/SimBindProfiles/increasedBindingRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: increasedBindingRegions
> ### Title: Classify two Binding Profiles - Increased Binding
> ### Aliases: increasedBindingRegions
> 
> ### ** Examples
> 
>   dataPath <- system.file("data",package="SimBindProfiles")
>   load(file.path(dataPath,"SGR.RData"))
>   overcompBC <- increasedBindingRegions(SGR, sgrset=c(2,3), bound.cutoff=1.86, diff.cutoff=1.4, 
+                 probes=10, probe.max.spacing=200)

Increased Binding comparison of SoxN-DDam vs DDam 

Filter data into regions...
Writing SoxN-DDam.vs.DDam.increasedBinding_b1.86d1.4v10g200.bed ,regions = 2 ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>