Starr (version 1.28.0)

plotcmarrt: 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

Value

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

Details

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

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,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)