plotcmarrt {Starr} | R Documentation

## Histogram of p-values and normal QQ plots for standardized MA statistics

### Description

Plot the histograms of p-values and normal QQ plots under correlation structure and independence.

### Usage

    plotcmarrt(cmarrt.ma, freq=FALSE)

### Arguments

`cmarrt.ma` | output object from `cmarrt.ma`.
`freq` | see ?hist

### Details

Diagnostic plots for comparing the distribution of standardized MA statistics under correlation and independence.

### Value

Histogram of p-values and normal QQ plots under correlation structure and independence.

### Note

If the normal quantile-quantile plot deviates from the reference line for unbound probes, this indicates that Gaussian approximation is not suitable for analyzing this data.

### 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`,`qqnorm`

### 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')

    # plotcmarrt(peaks)

[Package Starr version 1.43.0 Index]