Starr (version 1.28.0)

cmarrt.peak: Obtain bound regions for a given error rate control

Description

Obtain bound regions under a given error rate control using correction method from p.adjust.

Usage

cmarrt.peak(cmarrt.ma, alpha, method, minrun, asCherList=FALSE)

Arguments

cmarrt.ma

output object from cmarrt.ma.

alpha

error rate control for declaring bound region.

method

correction method inherited from p.adjust.

minrun

minimum number of probes to be called a bound region.

asCherList

If TRUE, result is returned as class cherList. See Ringo, for further description.

Value

cmarrt.bound

list of bound regions obtained under correlation structure.

indep.bound

list of bound regions obtained under independence (ignoring correlation).

Details

The function returns two objects, cmarrt.bound and indep.bound. Each object is a list of bound regions which can be accessed by $chr (chromosome), $peak.start (start coordinate of each bound region), $peak.stop (stop coordinate of each bound region), $n.probe (number of probes within each bound region), $min.pv (minimum p-values of each bound region), $ave.pv (average p-values of each bound region).

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,p.adjust

Examples

# dataPath <- system.file("extdata", package="Starr")
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

# cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), 
# 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
# names <- c("rpb3_1", "wt_1","rpb3_2")
# type <- c("IP", "CONTROL", "IP")
# rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)

# ips <- rpb3Chr1$type == "IP"
# controls <- rpb3Chr1$type == "CONTROL"

# rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")
# description <- c("Rpb3vsWT")
# rpb3_rankpercentile_ratio <- getRatio(rpb3_rankpercentile, ips, controls, description, fkt=median, featureData=FALSE)

# probeAnnoChr1 <- bpmapToProbeAnno(bpmapChr1)
# peaks <- cmarrt.ma(rpb3_rankpercentile_ratio, probeAnnoChr1, chr=NULL, M=NULL,250,window.opt='fixed.probe')
# peaklist <- cmarrt.peak(peaks)