backgd.sd: Background parameters (internal function)

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

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 Biocomputing13:515-526.

See Also

cmarrt.ma

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