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Last data update: 2014.03.03

R: Max-gap-min-run algorithm for 2 states segmentation

maxGapminRun

R Documentation

Max-gap-min-run algorithm for 2 states segmentation

Description

A custom Max-gap-min-run implementation using physical position for gap and run length calculation.

Usage

maxGapminRun(x, xPos = NULL, xRange = NULL, cutoff = NULL, q = 0.9, high=TRUE, minrun = 5, maxgap = 2, splitLen = Inf, na.rm=TRUE)

Arguments

`x`	a numeric vector for the input signal
`xPos`	a numeric vector, same length as x, carrying positional information for each element of x
`xRange`	an `IRanges` object, same length as x, carrying range information for each element of x
`cutoff`	numeric value used as cut-off, optional if `q` is specified
`q`	numeric value used to derive cut-off of x, as the `q` quantile of x , optional if `cutoff` is specified
`high`	TRUE if the `cutoff` or `q` here is the lower bound and values greater than the threshold are considered
`minrun`	minimum run length for the resulting segments
`maxgap`	maximum genomic distance below which two adjacent qualified tiles can be joined
`splitLen`	numeric value, maximum length of segments, split if too long
`na.rm`	`TRUE` if `NA` value should be ignored

Details

A custom Max-gap-min-run implementation using physical position for gap and run length calculation.

Value

a list of segment starts and ends indices

`IS`	the start index for each segment
`IE`	the end index for each segment
`CUTOFF`	the cutoff value used in the run
`MG`	the parameter value for `maxgap`
`MR`	the parameter value for `minrun`
`SPL`	the parameter value for `splitLen`

Author(s)

Yang Du

Examples

	x<-rpois(50, 10)
	xpos<-rnorm(50, 300, 100)
	xpos<-xpos[order(xpos)]
	maxGapminRun(x, xpos, cutoff=9.5, maxgap=30, minrun=100)

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(biomvRCNS)
Loading required package: IRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biomvRCNS/maxGapminRun.Rd_%03d_medium.png", width=480, height=480)
> ### Name: maxGapminRun
> ### Title: Max-gap-min-run algorithm for 2 states segmentation
> ### Aliases: maxGapminRun
> 
> ### ** Examples
> 
> 	x<-rpois(50, 10)
> 	xpos<-rnorm(50, 300, 100)
> 	xpos<-xpos[order(xpos)]
> 	maxGapminRun(x, xpos, cutoff=9.5, maxgap=30, minrun=100)
$IS
integer(0)

$IE
integer(0)

$CUTOFF
[1] 9.5

$MG
[1] 30

$MR
[1] 100

$SPL
[1] Inf

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>