## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width=6, fig.height=6, fig.align = "center" ) ## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----eval=FALSE--------------------------------------------------------------- # # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("regioneReloaded") # ## ----setup-------------------------------------------------------------------- library("regioneReloaded") ## ----load _data, eval=FALSE--------------------------------------------------- # #NOT RUN # # set.seed(42) # cw_Alien_ReG<-crosswisePermTest(Alist = AlienRSList_narrow, # sampling = FALSE, # mc.cores= 25, # ranFUN = "resampleGenome", # evFUN = "numOverlaps", # genome = AlienGenome, # ntimes= 1000 # ) # # ## ----------------------------------------------------------------------------- data("cw_Alien") cw_Alien_ReG<-makeCrosswiseMatrix(cw_Alien_ReG, pvcut = 1) plotCrosswiseMatrix(cw_Alien_ReG) ## ----------------------------------------------------------------------------- AlienGenome <- toGRanges(data.frame( chr = c("AlChr1", "AlChr2", "AlChr3", "AlChr4"), start = c(rep(1, 4)), end = c(2e6, 1e6, 5e5, 1e5) )) ## ----------------------------------------------------------------------------- gnm <- AlienGenome nreg=100 regA <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = gnm ) regB <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50 , non.overlapping = TRUE, genome = gnm ) regC <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = gnm ) ## ----------------------------------------------------------------------------- vectorPerc <- seq(0.1, 0.9, 0.1) RsetA <- similarRegionSet( GR = regA, name = "regA", genome = gnm, vectorPerc = vectorPerc ) RsetB <- similarRegionSet( GR = regB, name = "regB", genome = gnm, vectorPerc = vectorPerc ) RsetC <- similarRegionSet( GR = regC, name = "regC", genome = gnm, vectorPerc = vectorPerc ) ## ----------------------------------------------------------------------------- vectorPerc2 <- seq(0.2, 0.8, 0.2) regAB <- c(sample(regA, nreg / 2), sample(regB, nreg / 2)) RsetAB <- similarRegionSet( GR = regAB, name = "regAB", genome = gnm, vectorPerc = vectorPerc2 ) ## ----------------------------------------------------------------------------- reg_no_A <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = subtractRegions(gnm, regA) ) reg_no_B <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = subtractRegions(gnm, regB) ) reg_no_C <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = subtractRegions(gnm, regC) ) reg_no_AB <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = subtractRegions(gnm, c(regA, regB)) ) reg_no_ABC <- createRandomRegions( nregions = nreg, length.mean = 100, length.sd = 50, non.overlapping = TRUE, genome = subtractRegions(gnm, c(regA, regB, regC)) ) ## ----------------------------------------------------------------------------- dst <- sample(c(-300,300),length(regA),replace = TRUE) regD <- regioneR::toGRanges( data.frame( chr=as.vector(GenomeInfoDb::seqnames(regA)), start = start(regA) + dst, end = end (regA) + dst ) ) RsetD <- similarRegionSet( GR = regD, name = "regD", genome = gnm, vectorPerc = vectorPerc2 ) ## ----------------------------------------------------------------------------- Rset_NO <- list(reg_no_A, reg_no_B, reg_no_C, reg_no_AB, reg_no_ABC) names(Rset_NO) <- c("reg_no_A", "reg_no_B", "reg_no_C", "reg_no_AB", "reg_no_ABC") AlienRSList_narrow <- c(RsetA, RsetB, RsetC, RsetD, RsetAB, Rset_NO) summary(AlienRSList_narrow) ## ----------------------------------------------------------------------------- data("cw_Alien") getParameters(cw_Alien_ReG) ## ----eval=FALSE--------------------------------------------------------------- # # #NOT RUN # # set.seed(42) # cw_Alien_RaR <- crosswisePermTest( # Alist = AlienRSList_narrow, # Blist = AlienRSList_narrow, # sampling = FALSE, # genome = AlienGenome, # per.chromosome=TRUE, # ranFUN = "randomizeRegions", # evFUN = "numOverlaps", # ntimes= 1000, # mc.cores = 20 # ) # # # set.seed(42) # cw_Alien_ReR <- crosswisePermTest( # Alist = AlienRSList_narrow, # Blist = AlienRSList_narrow, # sampling = FALSE, # genome = AlienGenome, # per.chromosome=TRUE, # ranFUN = "resampleRegions", # evFUN = "numOverlaps", # ntimes= 1000, # mc.cores = 20 # ) # # set.seed(42) # cw_Alien_ReG <- crosswisePermTest( # Alist = AlienRSList_narrow, # Blist = AlienRSList_narrow, # sampling = FALSE, # genome = AlienGenome, # per.chromosome=TRUE, # ranFUN = "resampleGenome", # evFUN = "numOverlaps", # ntimes= 100, # mc.cores = 20 # ) # # # # ## ----------------------------------------------------------------------------- cw_Alien_RaR <- makeCrosswiseMatrix(cw_Alien_RaR) cw_Alien_ReG <- makeCrosswiseMatrix(cw_Alien_ReG) cw_Alien_ReR <- makeCrosswiseMatrix(cw_Alien_ReR) ## ----------------------------------------------------------------------------- modX <- getHClust(cw_Alien_ReG,hctype = "rows") modY <- getHClust(cw_Alien_ReG,hctype = "cols") X<-modX$labels[modX$order] Y<-modY$labels[modX$order] ord<-list(X=X,Y=Y) p_ReG <- plotCrosswiseMatrix(cw_Alien_ReG, matrix_type = "association", ord_mat = ord) p_ReR <- plotCrosswiseMatrix(cw_Alien_ReR, matrix_type = "association", ord_mat = ord) plot(p_ReG) plot(p_ReR) ## ----------------------------------------------------------------------------- plot(modX,cex = 0.8) ## ----------------------------------------------------------------------------- p_ReG_cor <- plotCrosswiseMatrix(cw_Alien_ReG, matrix_type = "correlation", ord_mat = ord) # p_ReR_cor <- plotCrosswiseMatrix(cw_Alien_ReR, matrix_type = "correlation", ord_mat = ord) plot(p_ReG_cor) # plot(p_ReR_cor) ## ----------------------------------------------------------------------------- plotSinglePT(cw_Alien_ReG, RS1 = "regA", RS2 = "regA_05") ## ----------------------------------------------------------------------------- p_sPT1 <- plotSinglePT(cw_Alien_ReG, RS1 = "regA", RS2 = "regC") plot(p_sPT1) ## ----------------------------------------------------------------------------- set.seed(42) plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="PCA") ## ----------------------------------------------------------------------------- set.seed(42) p_cdr_hc <- plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="PCA", clust_met = "hclust") # set.seed(42) # p_cdr_pam <- plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="PCA", clust_met = "pam") plot(p_cdr_hc) # plot(p_cdr_pam) ## ----------------------------------------------------------------------------- lsRegSet<-list(regA="regA",regB="regB",regC="regC") set.seed(42) plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="PCA",listRS = lsRegSet) set.seed(42) plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="PCA",listRS = lsRegSet,ellipse = TRUE, emphasize =TRUE) set.seed(67) plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="tSNE",listRS = lsRegSet,ellipse = TRUE, emphasize =TRUE) set.seed(67) plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="UMAP",listRS = lsRegSet,ellipse = TRUE, emphasize =TRUE) ## ----------------------------------------------------------------------------- set.seed(67) silTable <- plotCrosswiseDimRed(cw_Alien_ReG, nc = 6, type="UMAP",listRS = lsRegSet,return_table = TRUE) silTable ## ----eval=FALSE--------------------------------------------------------------- # # #NOT RUN # mlz_Alien_ReG<-multiLocalZscore(A = AlienRSList_narrow$regA, # Blist = AlienRSList_narrow, # ranFUN = "resampleGenome", # evFUN = "numOverlaps", # window = 100, # step = 1, # max_pv = 1, # genome = AlienGenome) ## ----------------------------------------------------------------------------- getParameters(mLZ_regA_ReG) mlz_Me <- getMultiEvaluation(rR = mLZ_regA_ReG ) head(mlz_Me$resumeTable) ## ----------------------------------------------------------------------------- mLZ_regA_ReG <- makeLZMatrix(mLZ_regA_ReG) plot(getHClust(mLZ_regA_ReG),cex = 0.8) ## ----------------------------------------------------------------------------- plotLocalZScoreMatrix(mLZ_regA_ReG, maxVal = "max") ## ----------------------------------------------------------------------------- plotSingleLZ(mLZ = mLZ_regA_ReG, RS =c("regA"), smoothing = TRUE) ## ----------------------------------------------------------------------------- plotSingleLZ(mLZ = mLZ_regA_ReG,RS =c("regA","regA_02","regA_06","regA_08","regD"),smoothing = TRUE) ## ----------------------------------------------------------------------------- # average of the widths of AlienRSList_narrow do.call("c",lapply(lapply(AlienRSList_narrow, width),mean)) # average of the widths of AlienRSList_broad do.call("c",lapply(lapply(AlienRSList_broad, width),mean)) ## ----eval=FALSE--------------------------------------------------------------- # # ##NOT RUN # cw_Alien_RaR_no_Square <- crosswisePermTest( # Alist = AlienRSList_narrow, # Blist = AlienRSList_broad, # sampling = FALSE, # genome = AlienGenome, # per.chromosome=TRUE, # ranFUN = "resampleGenome", # evFUN = "numOverlaps", # ntimes= 100, # mc.cores = 6 # ) # # ### ## ----------------------------------------------------------------------------- cw_Alien_ReG_no_Square <- makeCrosswiseMatrix(cw_Alien_ReG_no_Square) plotCrosswiseMatrix(cw_Alien_ReG_no_Square) ## ----eval=FALSE--------------------------------------------------------------- # # #NOT RUN # mLZ_regA_ReG_br<-multiLocalZscore(A = # AlienRSList_narrow$regA, # Blist = AlienRSList_broad, # ranFUN = "resampleGenome", # genome = AlienGenome, # window = 5000, # step =100) # ## ## ----------------------------------------------------------------------------- mLZ_regA_ReG_br<-makeLZMatrix(mLZ_regA_ReG_br) plotLocalZScoreMatrix(mLZ_regA_ReG_br) ## ----------------------------------------------------------------------------- plotSingleLZ(mLZ = mLZ_regA_ReG_br,RS =c("regA_br","regA_br_02","regA_br_06","regA_br_08","regD_br"), smoothing = TRUE) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()