biomvRCNS (version 1.12.0)

maxGapminRun: 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

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

Details

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

See Also

biomvRhsmm biomvRseg biomvRmgmr

Examples

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