## ----setup_knitr, include = FALSE, cache = FALSE------------------------------ library(BiocStyle) # Decide whether to display parts for BioC (TRUE) or F1000 (FALSE) on.bioc <- TRUE library(knitr) # Use fig.width = 7 for html and fig.width = 6 for pdf fig.width <- ifelse(on.bioc, 8, 6) knitr::opts_chunk$set(cache = 2, warning = FALSE, message = FALSE, error = FALSE, cache.path = "cache/", fig.path = "figure/", fig.width = fig.width) ## ----------------------------------------------------------------------------- library(CSSQ) regionBed <- read.table(system.file("extdata", "chr19_regions.bed", package="CSSQ",mustWork = TRUE)) sampleInfo <- read.table(system.file("extdata", "sample_info.txt", package="CSSQ",mustWork = TRUE),sep="\t",header=TRUE) head(regionBed) sampleInfo ## ----------------------------------------------------------------------------- countData <- getRegionCounts(system.file("extdata", "chr19_regions.bed", package="CSSQ"),sampleInfo,sampleDir = system.file("extdata", package="CSSQ")) countData head(assays(countData)$countData) colData(countData) rowRanges(countData) ## ----------------------------------------------------------------------------- countData <- loadCountData(system.file("extdata", "sample_count_data.txt", package="CSSQ",mustWork = TRUE),system.file("extdata", "chr19_regions.bed", package="CSSQ"),sampleInfo) countData head(assays(countData)$countData) colData(countData) rowRanges(countData) ## ----------------------------------------------------------------------------- ansCountData <- ansTransform(countData) ansCountData head(assays(ansCountData)$ansCount) ## ----------------------------------------------------------------------------- normInfo <- normalizeData(ansCountData,numClusters=4) normInfo head(assays(normInfo)$normCount) ## ----------------------------------------------------------------------------- result <- DBAnalyze(normInfo,comparison=c("HSMM","HESC")) result ## ----------------------------------------------------------------------------- #To let CSSQ calculate the counts processedData <- preprocessData(system.file("extdata", "chr19_regions.bed", package="CSSQ"),system.file("extdata", "sample_info.txt", package="CSSQ"),sampleDir = system.file("extdata", package="CSSQ"),numClusters=4,noNeg=TRUE,plotData=FALSE) #To provide CSSQ with the counts processedData <- preprocessData(system.file("extdata", "chr19_regions.bed", package="CSSQ"),system.file("extdata", "sample_info.txt", package="CSSQ"),inputCountData = system.file("extdata", "sample_count_data.txt", package="CSSQ",mustWork = TRUE),numClusters=4,noNeg=TRUE,plotData=FALSE) #To find differential binding sites result <- DBAnalyze(processedData,comparison=c("HSMM","HESC")) processedData result ## ----------------------------------------------------------------------------- sessionInfo()