## ---- eval = FALSE------------------------------------------------------------ # # install.packages("BiocManager") # BiocManager::install("sevenC") ## ---- results = "hide", message = FALSE--------------------------------------- library(sevenC) # load provided CTCF motifs in human genome motifs <- motif.hg19.CTCF.chr22 # get motifs pairs gi <- prepareCisPairs(motifs) ## ----eval = FALSE, echo = TRUE------------------------------------------------ # # # use example ChIP-seq bigWig file # bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", # package = "sevenC") # # # add ChIP-seq coverage and compute correaltion at motif pairs # gi <- addCor(gi, bigWigFile) ## ----eval = TRUE, echo = FALSE------------------------------------------------ # check if on windows to prevent bigWig reading errors from rtracklayer if (.Platform$OS.type == 'windows') { # use motif data with ChIP-seq coverage motifs <- motif.hg19.CTCF.chr22.cov gi <- prepareCisPairs(motifs) gi <- addCovCor(gi) } else { # use example ChIP-seq bigWig file bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC") # add ChIP-seq coverage and compute correaltion at motif pairs gi <- addCor(gi, bigWigFile) } ## ----------------------------------------------------------------------------- # predict looping interactions among all motif pairs loops <- predLoops(gi) ## ---- results = "hide", message = FALSE--------------------------------------- library(sevenC) # load provided CTCF motifs motifs <- motif.hg19.CTCF.chr22 ## ----------------------------------------------------------------------------- # use example ChIP-seq bigWig file bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC") ## ----eval = FALSE------------------------------------------------------------- # # read ChIP-seq coverage # motifs <- addCovToGR(motifs, bigWigFile) ## ----eval = TRUE, echo = FALSE------------------------------------------------ # check if OS is windows if (.Platform$OS.type == 'windows') { motifs <- motif.hg19.CTCF.chr22.cov } else { # read ChIP-seq coverage motifs <- addCovToGR(motifs, bigWigFile) } ## ----------------------------------------------------------------------------- motifs$chip ## ----------------------------------------------------------------------------- gi <- prepareCisPairs(motifs, maxDist = 10^6) gi ## ----------------------------------------------------------------------------- # add ChIP-seq coverage and compute correaltion at motif pairs gi <- addCovCor(gi) ## ----------------------------------------------------------------------------- loops <- predLoops(gi) loops ## ---- results = "hide", message = FALSE--------------------------------------- library(GenomicInteractions) # export to output file export.bedpe(loops, "loop_interactions.bedpe", score = "pred") ## ----eval = FALSE, echo = TRUE------------------------------------------------ # # load provided CTCF motifs # motifs <- motif.hg19.CTCF.chr22 # # # use example ChIP-seq coverage file # bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", # package = "sevenC") # # # add ChIP-seq coverage # motifs <- addCovToGR(motifs, bigWigFile) # # # build motif pairs # gi <- prepareCisPairs(motifs, maxDist = 10^6) # # # add correaltion of ChIP-signal # gi <- addCovCor(gi) ## ----eval = TRUE, echo = FALSE------------------------------------------------ # check if OS is windows if (.Platform$OS.type == 'windows') { motifs <- motif.hg19.CTCF.chr22.cov } else { # load provided CTCF motifs motifs <- motif.hg19.CTCF.chr22 # use example ChIP-seq coverage file bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC") # add ChIP-seq coverage motifs <- addCovToGR(motifs, bigWigFile) } gi <- prepareCisPairs(motifs, maxDist = 10^6) # add correaltion of ChIP-signal gi <- addCovCor(gi) ## ---- message = FALSE--------------------------------------------------------- # parse known loops knownLoopFile <- system.file("extdata", "GM12878_HiCCUPS.chr22_1-30000000.loop.txt", package = "sevenC") knownLoops <- parseLoopsRao(knownLoopFile) ## ----------------------------------------------------------------------------- # add known loops gi <- addInteractionSupport(gi, knownLoops) ## ----------------------------------------------------------------------------- fit <- glm( formula = loop ~ cor_chip + dist + strandOrientation, data = mcols(gi), family = binomial() ) ## ----------------------------------------------------------------------------- # add predict loops gi <- predLoops( gi, formula = loop ~ cor_chip + dist + strandOrientation, betas = coef(fit), cutoff = NULL ) ## ----------------------------------------------------------------------------- gi ## ---- fig.width = 3, fig.height = 4------------------------------------------- boxplot(gi$pred ~ gi$loop, ylab = "Predicted interaction probability") ## ----------------------------------------------------------------------------- sessionInfo()