maxGapminRun {biomvRCNS} | 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

### 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)

[Package biomvRCNS version 1.32.0 Index]