backgd.sd {Starr} | R Documentation

## Background parameters (internal function)

### Description

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

### Usage

    backgd.sd(regID, logR, M = NULL, chr, start, stop)

### Arguments

`regID` | consecutive genomic region ID.
`logR` | probe measurements, e.g., log ratios, t-statistics.
`M` | rough estimate of the percentage of bound probes. If unknown, leave it NULL.
`chr` | chromosome ID of each probe.
`start` | start coordinate of each probe.
`stop` | stop coordinate of each probe.

### Value

`center` | estimated center of the unbound probes.
`sigma` | estimated standard deviation of the unbound probes.
`rho` | autocorrelation functions for maximum window size/lag of 30 probes.

### 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 1.36.0 Index]