ma.stat {Starr} | R Documentation

## Compute moving average statistics and p-values

### 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 Biocomputing 13:515-526.

### See Also

`cmarrt.ma`

[Package Starr version 1.38.0 Index]