## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----quick-start, message=FALSE, warning=FALSE---------------------------- library(InTAD) # normalized enhancer signals table enhSel[1:3,1:3] # enhancer signal genomic coordinates as.data.frame(enhSelGR[1:3]) # gene expression normalized counts rpkmCountsSel[1:3,1:3] # gene coordiantes as.data.frame(txsSel[1:3]) # additional sample info data.frame head(mbAnnData) ## ----input-check1, warning=FALSE------------------------------------------ summary(colnames(rpkmCountsSel) == colnames(enhSel)) ## ----input-check2, warning=FALSE------------------------------------------ # compare number of signal regions and in the input table length(enhSelGR) == nrow(enhSel) ## ----test, warning=FALSE-------------------------------------------------- inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel,mbAnnData) ## ----test2, warning=FALSE------------------------------------------------- inTadSig ## ----filter-genes, warning=FALSE------------------------------------------ # filter gene expression inTadSig <- filterGeneExpr(inTadSig, checkExprDistr = TRUE) ## ----tad1, warning=FALSE-------------------------------------------------- # IMR90 hg19 TADs head(tadGR) ## ----tad2, warning=FALSE-------------------------------------------------- # combine signals and genes in TADs inTadSig <- combineInTAD(inTadSig, tadGR) ## ----cor, warning=FALSE--------------------------------------------------- par(mfrow=c(1,2)) # option to combine plots in the graph # perform correlation anlaysis corData <- findCorrelation(inTadSig,plot.proportions = TRUE) ## ----cor2, warning=FALSE-------------------------------------------------- head(corData,5) ## ----plot0, warning=FALSE-------------------------------------------------- # example enhancer in correlation with GABRA5 cID <- "chr15:26372163-26398073" selCorData <- corData[corData$peakid == cID, ] selCorData[ selCorData$name == "GABRA5", ] ## ----plot1,fig.align = "center", warning=FALSE----------------------------- plotCorrelation(inTadSig, cID, "GABRA5", xLabel = "RPKM gene expr log2", yLabel = "H3K27ac enrichment log2", colByPhenotype = "Subgroup") ## ----plot3, fig.align = "center", warning=FALSE---------------------------- plotCorAcrossRef(inTadSig,corData, targetRegion = GRanges("chr15:25000000-28000000"), tads = tadGR) ## ----plot4, fig.align = "center", warning=FALSE---------------------------- plotCorAcrossRef(inTadSig,corData, targetRegion = GRanges("chr15:25000000-28000000"), showCorVals = TRUE, tads = tadGR) ## ----plot5, fig.align = "center", warning=FALSE---------------------------- plotCorAcrossRef(inTadSig,corData, targetRegion = GRanges("chr15:25000000-28000000"), showCorVals = TRUE, symmetric = TRUE, tads = tadGR) ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()