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Last data update: 2014.03.03

R: Segment a vector into positive, zero, and negative regions

getSegments

R Documentation

Segment a vector into positive, zero, and negative regions

Description

Given two cutoffs, L and U, this function divides a numerical vector into contiguous parts that are above U, between L and U, and below L.

Usage

getSegments(x, f = NULL, cutoff = quantile(abs(x), 0.99),
            assumeSorted = FALSE, verbose = FALSE)

Arguments

`x`	A numeric vector.
`f`	A factor used to pre-divide `x` into pieces. Each piece is then segmented based on the cutoff. Setting this to `NULL` says that there is no pre-division. Often, `clusterMaker` is used to define this factor.
`cutoff`	a numeric vector of length either 1 or 2. If length is 1, U (see details) will be cutoff and L will be -cutoff. Otherwise it specifies L and U. The function will furthermore always use the minimum of cutoff for L and the maximum for U.
`assumeSorted`	This is a statement that the function may assume that the vector `f` is sorted. Allowing the function to make this assumption may increase the speed of the function slightly.
`verbose`	Should the function be verbose?

Details

This function is used to find the indexes of the ‘bumps’ in functions such as bumphunter.

x is a numeric vector, which is converted into three levels depending on whether x>=U (‘up’), L<x<U (‘zero’) or x<=L (‘down’), with L and U coming from cutoff. We assume that adjacent entries in x are next to each other in some sense. Segments, consisting of consecutive indices into x (ie. values between 1 and length(x)), are formed such that all indices in the same segment belong to the same level of f and have the same discretized value of x.

In other words, we can use getSegments to find runs of x belonging to the same level of f and with all of the values of x either above U, between L and U, or below L.

Value

A list with three components, each a list of indices. Each component of these lists represents a segment and this segment is represented by a vector of indices into the original vectors x and f.

`upIndex:`	a list with each entry an index of contiguous values in the same segment. These segments have values of `x` above U.
`dnIndex:`	a list with each entry an index of contiguous values in the same segment. These segments have values of `x` below L.
`zeroIndex:`	a list with each entry an index of contiguous values in the same segment. These segments have values of `x` between L and U.

Author(s)

Rafael A Irizarry and Kasper Daniel Hansen

Examples

x <- 1:100
y <- sin(8*pi*x/100)
chr <- rep(1, length(x))
indexes <- getSegments(y, chr, cutoff=0.8)
plot(x, y, type="n")
for(i in 1:3){
   ind <- indexes[[i]]
   for(j in seq(along=ind)) {
      k <- ind[[j]]
      text(x[k], y[k], j, col=i)
   }
}
abline(h=c(-0.8,0.8))

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(bumphunter)
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/bumphunter/getSegments.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getSegments
> ### Title: Segment a vector into positive, zero, and negative regions
> ### Aliases: getSegments
> 
> ### ** Examples
> 
> x <- 1:100
> y <- sin(8*pi*x/100)
> chr <- rep(1, length(x))
> indexes <- getSegments(y, chr, cutoff=0.8)
> plot(x, y, type="n")
> for(i in 1:3){
+    ind <- indexes[[i]]
+    for(j in seq(along=ind)) {
+       k <- ind[[j]]
+       text(x[k], y[k], j, col=i)
+    }
+ }
> abline(h=c(-0.8,0.8))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>