DBAnalyze {CSSQ} | R Documentation |
This is a wrapper function that performs the different parts of
differential binding analysis. Returns a
GRanges-class
with a calculated P-value and
Fold change for each region.
DBAnalyze(preprocessedData, comparison)
preprocessedData |
A
|
comparison |
A vector containing the comparison to be made. Names here need to correspond to the sample groups in the sample file (Eg. c("G1",G2") means the comparison G1/G2). |
A GRanges-class
object
containing the regions along with their P-values and Fold change for the
comparison.
exRange <- GRanges(seqnames=c("chr1","chr2","chr3","chr4"), ranges=IRanges(start=c(1000,2000,3000,4000),end=c(1500,2500,3500,4500))) sampleInfo <- read.table(system.file("extdata", "sample_info.txt", package="CSSQ",mustWork = TRUE),sep="\t",header=TRUE) exCount <- matrix(c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16),nrow=4,ncol=4) exData <- SummarizedExperiment(assays = list(ansCount=exCount), rowRanges=exRange,colData=sampleInfo) normExData <- normalizeData(exData,numClusters=2) res <- DBAnalyze(normExData,comparison=c("HSMM","HESC")) res