rm.small.peak: Remove bound regions which consist of too few probes
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Details Value Author(s) References See Also

An internal function to be used by cmarrt.peak.

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

`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.

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

`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.

Pei Fen Kuan, Adam Hinz

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 Biocomputing13:515-526.

cmarrt.peak

Starr documentation built on April 28, 2020, 7:52 p.m.