cmarrt.peak {Starr} | R Documentation

## 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.

### 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 Biocomputing 13:515-526.

### 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)

[Package Starr version 1.43.0 Index]