## ----knitr, echo=FALSE, results="hide"---------------------------------------- library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="hide", fig.width=4,fig.height=4.5, message=FALSE) ## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----loadSoggi, echo=FALSE------------------------------------------------- library("soGGi") ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----options, results="hide", echo=FALSE-------------------------------------- options(digits=3, width=80, prompt=" ", continue=" ") ## ----quick1, eval=FALSE , fig.width=10, fig.height=6-------------------------- # library(soGGi) # chipExample <- regionPlot("pathToBAM/mybam.bam",myGRangesObject,format="bam") ## ----quick1_1, eval=TRUE , fig.width=10, fig.height=6------------------------- library(soGGi) data(chipExampleBig) chipExampleBig ## ----quick1_2, eval=TRUE , fig.width=10, fig.height=6------------------------- chipExampleBig[[1]] chipExampleBig$highdnase ## ----quick1_3, eval=TRUE , fig.width=10, fig.height=6------------------------- c(chipExampleBig[[1]],chipExampleBig[[2]]) rbind(chipExampleBig[[1]],chipExampleBig[[2]]) ## ----quicka, eval=TRUE , fig.width=10, fig.height=6--------------------------- plotRegion(chipExampleBig[[3]]) ## ----quick2, eval=TRUE , fig.width=10, fig.height=6--------------------------- library(ggplot2) plotRegion(chipExampleBig,colourBy="Sample", groupBy="Sample", freeScale=TRUE) ## ----quick2b, eval=TRUE , fig.width=10, fig.height=6-------------------------- library(ggplot2) plotRegion(chipExampleBig,colourBy="Sample", outliers=0.01, groupBy="Sample",freeScale=TRUE) ## ----quick3, eval=TRUE , fig.width=10, fig.height=6--------------------------- library(GenomicRanges) subsetsCharacter <- list(first25 = (as.vector(rowRanges(chipExampleBig[[1]])$name[1:25])), fourth25 = as.vector(rowRanges(chipExampleBig[[1]])$name[76:100])) subsetsGRanges <- GRangesList(low=(rowRanges(chipExampleBig[[1]])[1:25]), high=rowRanges(chipExampleBig[[2]])[76:100]) plotRegion(chipExampleBig[[1]],gts=subsetsCharacter,summariseBy = "name") plotRegion(chipExampleBig[[1]],gts=subsetsGRanges) ## ----quick4, eval=TRUE , fig.width=10, fig.height=6--------------------------- pol_Profiles <- c((chipExampleBig$highPol+chipExampleBig$midPol) , (chipExampleBig$highPol_Rep2+chipExampleBig$midPol_Rep2)) plotRegion(pol_Profiles,colourBy="Sample",outliers=0.01, groupBy="Sample", freeScale=TRUE) ## ----quick6, eval=TRUE , fig.width=10, fig.height=6--------------------------- log2Profiles <- log2(chipExampleBig) plotRegion(log2Profiles,colourBy="Sample",outliers=0.01, groupBy="Sample",freeScale=TRUE) ## ----quick6b, eval=TRUE , fig.width=10, fig.height=6-------------------------- log2Polhigh <- mean(log2Profiles$highPol, log2Profiles$highPol_Rep2) log2Polmid <- mean(log2Profiles$midPol, log2Profiles$midPol_Rep2) diffPol <- log2Polhigh-log2Polmid diffh3k9ac <- log2Profiles$highk9ac-log2Profiles$midk9ac plotRegion(c(diffPol,diffh3k9ac),colourBy="Sample",outliers=0.01, groupBy="Sample", freeScale=TRUE) ## ----quick7, eval=TRUE , fig.width=10, fig.height=6--------------------------- normHighPol <- normalise(c(chipExampleBig$highPol, chipExampleBig$highPol_Rep2), method="quantile",normFactors = 1) normMidPol <- normalise(c(chipExampleBig$midPol, chipExampleBig$midPol_Rep2), method="quantile",normFactors = 1) normPol <-c(normHighPol$highPol, normHighPol$highPol_Rep2, normMidPol$midPol, normMidPol$midPol_Rep2) plotRegion(normPol,colourBy="Sample",outliers=0.01, groupBy="Sample", freeScale=TRUE) ## ----quick8, eval=TRUE , fig.width=10, fig.height=5--------------------------- data(ik_Example) ik_Example peakSetCombinations <- groupByOverlaps(ik_Example) peakSetCombinations ## ----quick10, eval=TRUE , fig.width=10, fig.height=5-------------------------- data(ik_Profiles) ik_Profiles log2Ik_Profiles <- log2(ik_Profiles) plotRegion(log2Ik_Profiles,outliers=0.01,gts=peakSetCombinations, groupBy="Group",colourBy="Sample", freeScale=TRUE) plotRegion(log2Ik_Profiles[[1]] - log2Ik_Profiles[[2]] ,outliers=0.01,gts=peakSetCombinations, groupBy="Group", colourBy="Sample", freeScale=FALSE) ## ----sessionInfo, results='asis', eval=TRUE----------------------------------- toLatex(sessionInfo())