ma.stat: Compute moving average statistics and p-values

In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description

An internal function to be used by cmarrt.ma.

Usage

ma.stat(regID, chr, start, stop, logR, frag.length, center, sigma, rho, window.opt = "fixed.probe")

Arguments

regID	consecutive genomic region ID.
chr	chromosome ID of each probe.
start	start coordinate of each probe.
stop	stop coordinate of each probe.
logR	probe measurements, e.g., log ratio.
frag.length	average fragment length from sonication.
center	estimated center of the unbound probes from backgd.sd.
sigma	estimated standard deviation of the unbound probes backgd.sd.
rho	autocorrelation functions for maximum window size/lag of 30 probes backgd.sd.
window.opt	option for sliding window, either "fixed.probe" or "fixed.gen.dist". Default is 'fixed.probe'.

Value

ma	unstandardized moving average(MA) statistics.
z.cmarrt	standardized MA under correlation structure.
z.indep	standardized MA under independence (ignoring correlation structure).
pv.cmarrt	p-values of probes under correlation.
pv.indep	p-values of probes under independence (ignoring correlation structure).

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 Biocomputing13:515-526.

See Also

cmarrt.ma

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