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

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

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.

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).

Value

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

Note

The list of bound regions obtained under independence (ignoring the correlation structure) is for comparison. It is not recommended to use this list for downstream analysis.

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,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)

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