rm.small.peak {Starr} | R Documentation

## Remove bound regions which consist of too few probes

### Description

An internal function to be used by `cmarrt.peak`.

### Usage

    rm.small.peak(bdd.method, minrun, chr, start, stop, pv)

### Arguments

`bdd.method` | vector of 0's(unbound) or 1's(bound) for each probe.
`minrun` | minimum number of probes to be called a bound region.
`chr` | chromosome ID of each probe.
`start` | start coordinate of each probe.
`stop` | stop coordinate of each probe.
`pv` | p-values for each probe.

### Details

~~ If necessary, more details than the description above ~~

### Value

`bdd.method` | vector of 0's(unbound) or 1's(bound) for each probe.
`size:` | number of probes within each bound region.
`peak.start` | first probe location for each bound region.
`peak.end` | last probe location for each bound region.
`chr.start` | start chromosome for each bound region.
`chr.stop` | stop chromosome for each bound region.
`loc.start` | start coordinate for each bound region.
`loc.stop` | stop coordinate for each bound region.
`minPv` | minimum p-value for each bound region.
`avePv` | average p-value for each bound region.

### Author(s)

Pei Fen Kuan, Adam Hinz

### References

P.F. Kuan, H. Chun, S. Keles (2008). CMARRT: A tool for the analysiz of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pacific Symposium of Biocomputing 13:515-526.

### See Also

`cmarrt.peak`

[Package Starr version 1.40.0 Index]