MMDiff2 (version 1.0.2)

MMD: DBAmmd Object for Cfp1 example

Description

DBAmmd Object for Cfp1 example

Usage

data('MMD')

Examples

# data was created as follows:
## Not run: 
# library('MMDiff2')
# library('MMDiffBamSubset')
# # create metaData:
# ExperimentData <- list(genome='BSgenome.Mmusculus.UCSC.mm9',
#                       dataDir=system.file("extdata", package="MMDiffBamSubset"),
#                       sampleSheet="Cfp1.csv")
# MetaData <- list('ExpData' = ExperimentData)
# MMD <- DBAmmd(MetaData)
# data("Cfp1-Peaks")
# 
# MMD <- setRegions(MMD,Peaks)
# MMD <- getPeakReads(MMD,pairedEnd=FALSE, run.parallel=FALSE)
# 
# MMD <- DBAmmd(MetaData)
# MMD <- setRegions(MMD,Peaks)
# MMD <- getPeakReads(MMD,pairedEnd=FALSE, run.parallel=FALSE)
# MMD <- estimateFragmentCenters(MMD, shift=NULL, draw.on=FALSE)
# MMD <- compHists(MMD, bin.length=20)
# MMD <- compDists(MMD, dist.method = "MMD", run.parallel = FALSE)
# group1 <- Samples(MMD)$Condition==1
# names(group1) <- Samples(MMD)$SampleID
# group2 <- Samples(MMD)$Condition==2
# names(group2) <-  Samples(MMD)$SampleID
# con <- list(group1=group1,
#            group2=group2,
#            name1='WT-Resc',
#            name2='KO')
# 
# MMD <- compPvals(MMD, contrasts=list(con))
# ## End(Not run)