## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("maftools") ## ----loadlib, results='hide', message=FALSE----------------------------------- library(maftools) ## ----readmaf------------------------------------------------------------------ #path to TCGA LAML MAF file laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools') #clinical information containing survival information and histology. This is optional laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') laml = read.maf(maf = laml.maf, clinicalData = laml.clin) ## ----mafobject---------------------------------------------------------------- #Typing laml shows basic summary of MAF file. laml ## ----mafsummary, eval=FALSE--------------------------------------------------- # #Shows sample summry. # getSampleSummary(laml) # #Shows gene summary. # getGeneSummary(laml) # #shows clinical data associated with samples # getClinicalData(laml) # #Shows all fields in MAF # getFields(laml) # #Writes maf summary to an output file with basename laml. # write.mafSummary(maf = laml, basename = 'laml') ## ----summaryPlot,fig.height=4, fig.width=6------------------------------------ plotmafSummary(maf = laml, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE) ## ----oncoplot, fig.align='left',fig.height=3.5,fig.width=6, fig.align='left'---- #oncoplot for top ten mutated genes. oncoplot(maf = laml, top = 10) ## ----titv, fig.height=3, fig.width=4.2, eval = T, fig.align='left'------------ laml.titv = titv(maf = laml, plot = FALSE, useSyn = TRUE) #plot titv summary plotTiTv(res = laml.titv) ## ----lollipopPlot,fig.align='left', fig.width=4.5, fig.height=2.5------------- #lollipop plot for DNMT3A, which is one of the most frequent mutated gene in Leukemia. lollipopPlot( maf = laml, gene = 'DNMT3A', AACol = 'Protein_Change', showMutationRate = TRUE, labelPos = 882 ) ## ----lollipopPlot4, fig.align='left', fig.width=4.5, fig.height=2.5----------- #example data my_data = data.frame(pos = sample.int(912, 15, replace = TRUE), count = sample.int(30, 15, replace = TRUE)) head(my_data) lollipopPlot(data = my_data, gene = "DNMT3A") ## ----plotProtein,fig.align='left', fig.width=5, fig.height=1.2---------------- plotProtein(gene = "TP53", refSeqID = "NM_000546") ## ----rainfallPlot, results='hide', message=FALSE------------------------------ brca <- system.file("extdata", "brca.maf.gz", package = "maftools") brca = read.maf(maf = brca, verbose = FALSE) ## ----rainfallPlot2, fig.height=3,fig.width=6,fig.align='left'----------------- rainfallPlot(maf = brca, detectChangePoints = TRUE, pointSize = 0.4) ## ----tcgaCompare, fig.align='left', fig.height=3.25, fig.width=6, message=FALSE, results='hide'---- laml.mutload = tcgaCompare(maf = laml, cohortName = 'Example-LAML', logscale = TRUE, capture_size = 50) ## ----plotVaf, fig.align='left', fig.height=3, fig.width=3--------------------- plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU') ## ----readGistic--------------------------------------------------------------- gistic_res_folder <- system.file("extdata", package = "maftools") laml.gistic = readGistic(gisticDir = gistic_res_folder, isTCGA = TRUE) #GISTIC object laml.gistic ## ----gisticChromPlot, fig.width=4, fig.height=3, fig.align='left'------------- gisticChromPlot(gistic = laml.gistic, markBands = "all") ## ----coGisticChromPlot, fig.width=4, fig.height=5, fig.align='left'----------- coGisticChromPlot(gistic1 = laml.gistic, gistic2 = laml.gistic, g1Name = "AML-1", g2Name = "AML-2", type = 'Amp') ## ----gisticBubblePlot, fig.width=4, fig.height=3, fig.align='left'------------ gisticBubblePlot(gistic = laml.gistic) ## ----gisticOncoPlot, fig.align='left',fig.width=5, fig.height=3, eval=T------- gisticOncoPlot(gistic = laml.gistic, clinicalData = getClinicalData(x = laml), clinicalFeatures = 'FAB_classification', sortByAnnotation = TRUE, top = 10) ## ----segSummarize------------------------------------------------------------- laml.seg <- system.file("extdata", "LAML_CBS_segments.tsv.gz", package = "maftools") segSummarize_results = segSummarize(seg = laml.seg) ## ----plotCBSsegments, fig.height=2.5,fig.width=4,fig.align='left'------------- tcga.ab.009.seg <- system.file("extdata", "TCGA.AB.3009.hg19.seg.txt", package = "maftools") plotCBSsegments(cbsFile = tcga.ab.009.seg) ## ----somaticInteractions, message=FALSE, fig.height=5, fig.width=5------------ #exclusive/co-occurance event analysis on top 10 mutated genes. somaticInteractions(maf = laml, top = 25, pvalue = c(0.05, 0.1)) ## ----oncodrive, fig.align='default', fig.width=7,fig.height=5, message=F,results='hide', eval=T---- laml.sig = oncodrive(maf = laml, AACol = 'Protein_Change', minMut = 5, pvalMethod = 'zscore') ## ----------------------------------------------------------------------------- head(laml.sig) ## ----plotOncodrive, fig.align='left', fig.width=3.2, fig.height=3.2----------- plotOncodrive(res = laml.sig, fdrCutOff = 0.1, useFraction = TRUE, labelSize = 0.5) ## ----pfamDomains, fig.align='left', fig.width=4, fig.height=3----------------- laml.pfam = pfamDomains(maf = laml, AACol = 'Protein_Change', top = 10) #Protein summary (Printing first 7 columns for display convenience) laml.pfam$proteinSummary[,1:7, with = FALSE] #Domain summary (Printing first 3 columns for display convenience) laml.pfam$domainSummary[,1:3, with = FALSE] ## ----mafSurvival, fig.width=3, fig.height=3----------------------------------- #Survival analysis based on grouping of DNMT3A mutation status mafSurvival(maf = laml, genes = 'DNMT3A', time = 'days_to_last_followup', Status = 'Overall_Survival_Status', isTCGA = TRUE) ## ----survGroup---------------------------------------------------------------- #Using top 20 mutated genes to identify a set of genes (of size 2) to predict poor prognostic groups prog_geneset = survGroup(maf = laml, top = 20, geneSetSize = 2, time = "days_to_last_followup", Status = "Overall_Survival_Status", verbose = FALSE) print(prog_geneset) ## ----mafSurvGroup, fig.width=3, fig.height=3---------------------------------- mafSurvGroup(maf = laml, geneSet = c("DNMT3A", "FLT3"), time = "days_to_last_followup", Status = "Overall_Survival_Status") ## ----results='hide', message=FALSE-------------------------------------------- #Primary APL MAF primary.apl = system.file("extdata", "APL_primary.maf.gz", package = "maftools") primary.apl = read.maf(maf = primary.apl) #Relapse APL MAF relapse.apl = system.file("extdata", "APL_relapse.maf.gz", package = "maftools") relapse.apl = read.maf(maf = relapse.apl) ## ----mafCompare, fig.align='left'--------------------------------------------- #Considering only genes which are mutated in at-least in 5 samples in one of the cohort to avoid bias due to genes mutated in single sample. pt.vs.rt <- mafCompare(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary', m2Name = 'Relapse', minMut = 5) print(pt.vs.rt) ## ----forestPlot, fig.width=6, fig.height=4.5, fig.align='left'---------------- forestPlot(mafCompareRes = pt.vs.rt, pVal = 0.1) ## ----coOncoplot, fig.height=2.5,fig.width=6, eval=T, fig.align='left'--------- genes = c("PML", "RARA", "RUNX1", "ARID1B", "FLT3") coOncoplot(m1 = primary.apl, m2 = relapse.apl, m1Name = 'PrimaryAPL', m2Name = 'RelapseAPL', genes = genes, removeNonMutated = TRUE) ## ----coBarplot, fig.height=3, fig.width=4------------------------------------- coBarplot(m1 = primary.apl, m2 = relapse.apl, m1Name = "Primary", m2Name = "Relapse") ## ----lollipopPlot2, warning=FALSE, message=FALSE,fig.align='left', results='hide', fig.height=3.5, fig.width=5---- lollipopPlot2(m1 = primary.apl, m2 = relapse.apl, gene = "PML", AACol1 = "amino_acid_change", AACol2 = "amino_acid_change", m1_name = "Primary", m2_name = "Relapse") ## ----clinicalEnrichment------------------------------------------------------- fab.ce = clinicalEnrichment(maf = laml, clinicalFeature = 'FAB_classification') #Results are returned as a list. Significant associations p-value < 0.05 fab.ce$groupwise_comparision[p_value < 0.05] ## ----plotEnrichmentResults, fig.width=4, fig.height=3------------------------- plotEnrichmentResults(enrich_res = fab.ce, pVal = 0.05, geneFontSize = 0.5, annoFontSize = 0.6) ## ----drugInteractions, fig.height=3, fig.width=5------------------------------ dgi = drugInteractions(maf = laml, fontSize = 0.75) ## ----drugInteractions2-------------------------------------------------------- dnmt3a.dgi = drugInteractions(genes = "DNMT3A", drugs = TRUE) #Printing selected columns. dnmt3a.dgi[,.(Gene, interaction_types, drug_name, drug_claim_name)] ## ----OncogenicPathways, fig.width=7, fig.height=6----------------------------- pws = pathways(maf = laml, plotType = 'treemap') ## ----PlotOncogenicPathways, fig.width=6, fig.height=3.5----------------------- plotPathways(maf = laml, pathlist = pws) ## ----inferHeterogeneity, echo = TRUE, fig.align='left', fig.height=3.5, fig.width=4, eval=T---- #Heterogeneity in sample TCGA.AB.2972 library("mclust") tcga.ab.2972.het = inferHeterogeneity(maf = laml, tsb = 'TCGA-AB-2972', vafCol = 'i_TumorVAF_WU') print(tcga.ab.2972.het$clusterMeans) #Visualizing results plotClusters(clusters = tcga.ab.2972.het) ## ----plotClusters, fig.align='left', fig.height=3.5, fig.width=4, eval=T------ seg = system.file('extdata', 'TCGA.AB.3009.hg19.seg.txt', package = 'maftools') tcga.ab.3009.het = inferHeterogeneity(maf = laml, tsb = 'TCGA-AB-3009', segFile = seg, vafCol = 'i_TumorVAF_WU') #Visualizing results. Highlighting those variants on copynumber altered variants. plotClusters(clusters = tcga.ab.3009.het, genes = 'CN_altered', showCNvars = TRUE) ## ----trinucleotideMatrix, eval=TRUE------------------------------------------- #Requires BSgenome object library("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE) laml.tnm = trinucleotideMatrix(maf = laml, prefix = 'chr', add = TRUE, ref_genome = "BSgenome.Hsapiens.UCSC.hg19") ## ----plotApobecDiff, eval=TRUE, fig.height=3, fig.width=5--------------------- plotApobecDiff(tnm = laml.tnm, maf = laml, pVal = 0.2) ## ----echo=FALSE--------------------------------------------------------------- par(mar = c(2, 2, 2, 1)) plot(NA, xlim = c(1, 10), ylim = c(0, 30), frame.plot = FALSE, axes = FALSE, xlab = NA, ylab = NA) rect(xleft = 3, ybottom = 28, xright = 7, ytop = 30, col = grDevices::adjustcolor("gray70", alpha.f = 0.6), lwd = 1.2, border = "maroon") text(x = 5, y = 29, labels = "MAF", font = 2) arrows(x0 = 5, y0 = 28, x1 = 5, y1 = 26, length = 0.1, lwd = 2) text(x = 5, y = 25, labels = "trinucleotideMatrix()", font = 3) arrows(x0 = 5, y0 = 24, x1 = 5, y1 = 21, length = 0.1, lwd = 2) text(x = 5, y = 20, labels = "estimateSignatures()", font = 3) arrows(x0 = 5, y0 = 19, x1 = 5, y1 = 16, length = 0.1, lwd = 2) text(x = 5, y = 15, labels = "plotCophenetic()", font = 3) arrows(x0 = 5, y0 = 14, x1 = 5, y1 = 11, length = 0.1, lwd = 2) text(x = 5, y = 10, labels = "extractSignatures()", font = 3) arrows(x0 = 5, y0 = 9, x1 = 5, y1 = 6, length = 0.1, lwd = 2) text(x = 5, y = 5, labels = "compareSignatures()", font = 3) arrows(x0 = 5, y0 = 4, x1 = 5, y1 = 1, length = 0.1, lwd = 2) text(x = 5, y = 0, labels = "plotSignatures()", font = 3) ## ----estimateSignatures, fig.height=5, fig.width=5, eval=FALSE, message=FALSE---- # library('NMF') # laml.sign = estimateSignatures(mat = laml.tnm, nTry = 6) ## ----estimateSignatures2, fig.height=3, fig.width=3, eval=TRUE, message=FALSE, echo=FALSE, include=FALSE---- #Run main function with maximum 6 signatures. library('NMF') laml.sign = estimateSignatures(mat = laml.tnm, nTry = 6, pConstant = 0.1, plotBestFitRes = FALSE, parallel = 2) ## ----plotCophenetic, fig.width=3, fig.height=3, eval=TRUE--------------------- plotCophenetic(res = laml.sign) ## ----extractSignatures, eval=FALSE-------------------------------------------- # laml.sig = extractSignatures(mat = laml.tnm, n = 3) ## ----extractSignatures2, eval=TRUE, echo=FALSE-------------------------------- laml.sig = extractSignatures(mat = laml.tnm, n = 3, pConstant = 0.1, parallel = 2) ## ----compareSignatures, eval=TRUE--------------------------------------------- #Compate against original 30 signatures laml.og30.cosm = compareSignatures(nmfRes = laml.sig, sig_db = "legacy") #Compate against updated version3 60 signatures laml.v3.cosm = compareSignatures(nmfRes = laml.sig, sig_db = "SBS") ## ----pheatmap, fig.width=7, fig.height=2.5, fig.align='center', eval=TRUE----- library('pheatmap') pheatmap::pheatmap(mat = laml.og30.cosm$cosine_similarities, cluster_rows = FALSE, main = "cosine similarity against validated signatures") ## ----plotSignatures, fig.width=6, fig.height=4, fig.align='center', eval = TRUE---- maftools::plotSignatures(nmfRes = laml.sig, title_size = 1.2, sig_db = "SBS") ## ----legoplot3d, eval=FALSE--------------------------------------------------- # library("barplot3d") # #Visualize first signature # sig1 = laml.sig$signatures[,1] # barplot3d::legoplot3d(contextdata = sig1, labels = FALSE, scalexy = 0.01, sixcolors = "sanger", alpha = 0.5) ## ----annovarToMaf, eval=TRUE-------------------------------------------------- var.annovar = system.file("extdata", "variants.hg19_multianno.txt", package = "maftools") var.annovar.maf = annovarToMaf(annovar = var.annovar, Center = 'CSI-NUS', refBuild = 'hg19', tsbCol = 'Tumor_Sample_Barcode', table = 'ensGene') ## ----icgcSimpleMutationToMAF-------------------------------------------------- #Read sample ICGC data for ESCA esca.icgc <- system.file("extdata", "simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz", package = "maftools") esca.maf <- icgcSimpleMutationToMAF(icgc = esca.icgc, addHugoSymbol = TRUE) #Printing first 16 columns for display convenience. print(esca.maf[1:5,1:16, with = FALSE]) ## ----prepareMutSig, eval=FALSE------------------------------------------------ # laml.mutsig.corrected = prepareMutSig(maf = laml) # # Converting gene names for 1 variants from 1 genes # # Hugo_Symbol MutSig_Synonym N # # 1: ARHGAP35 GRLF1 1 # # Original symbols are preserved under column OG_Hugo_Symbol. ## ----subsetMaf---------------------------------------------------------------- #Extract data for samples 'TCGA.AB.3009' and 'TCGA.AB.2933' (Printing just 5 rows for display convenience) subsetMaf(maf = laml, tsb = c('TCGA-AB-3009', 'TCGA-AB-2933'), mafObj = FALSE)[1:5] ##Same as above but return output as an MAF object (Default behaviour) subsetMaf(maf = laml, tsb = c('TCGA-AB-3009', 'TCGA-AB-2933')) ## ----subsetMaf2--------------------------------------------------------------- #Select all Splice_Site mutations from DNMT3A and NPM1 subsetMaf(maf = laml, genes = c('DNMT3A', 'NPM1'), mafObj = FALSE,query = "Variant_Classification == 'Splice_Site'") #Same as above but include only 'i_transcript_name' column in the output subsetMaf(maf = laml, genes = c('DNMT3A', 'NPM1'), mafObj = FALSE, query = "Variant_Classification == 'Splice_Site'", fields = 'i_transcript_name') ## ----subsetMaf3--------------------------------------------------------------- #Select all samples with FAB clasification M4 in clinical data laml_m4 = subsetMaf(maf = laml, clinQuery = "FAB_classification %in% 'M4'") ## ----sampleSwaps, eval=FALSE-------------------------------------------------- # #Path to BAM files # bams = c( # "DBW-40-N.bam", # "DBW-40-1T.bam", # "DBW-40-2T.bam", # "DBW-40-3T.bam", # "DBW-43-N.bam", # "DBW-43-1T.bam" # ) # # res = maftools::sampleSwaps(bams = bams, build = "hg19") # # Fetching readcounts from BAM files.. # # Summarizing allele frequncy table.. # # Performing pairwise comparison.. # # Done! ## ----pairwise_comparison, eval=FALSE------------------------------------------ # res$pairwise_comparison ## ----------------------------------------------------------------------------- # X_bam Y_bam concordant_snps discordant_snps fract_concordant_snps cor_coef XY_possibly_paired # 1: DBW-40-1T DBW-40-2T 5488 571 0.9057600 0.9656484 Yes # 2: DBW-40-1T DBW-40-3T 5793 266 0.9560984 0.9758083 Yes # 3: DBW-40-1T DBW-43-N 5534 525 0.9133520 0.9667620 Yes # 4: DBW-40-2T DBW-40-3T 5853 206 0.9660010 0.9817475 Yes # 5: DBW-40-2T DBW-43-N 5131 928 0.8468394 0.9297096 Yes # 6: DBW-40-3T DBW-43-N 5334 725 0.8803433 0.9550670 Yes # 7: DBW-40-N DBW-43-1T 5709 350 0.9422347 0.9725684 Yes # 8: DBW-40-1T DBW-40-N 2829 3230 0.4669087 0.3808831 No # 9: DBW-40-1T DBW-43-1T 2796 3263 0.4614623 0.3755364 No # 10: DBW-40-2T DBW-40-N 2760 3299 0.4555207 0.3641647 No # 11: DBW-40-2T DBW-43-1T 2736 3323 0.4515597 0.3579747 No # 12: DBW-40-3T DBW-40-N 2775 3284 0.4579964 0.3770581 No # 13: DBW-40-3T DBW-43-1T 2753 3306 0.4543654 0.3721022 No # 14: DBW-40-N DBW-43-N 2965 3094 0.4893547 0.3839140 No # 15: DBW-43-1T DBW-43-N 2876 3183 0.4746658 0.3797829 No ## ----BAM_matches, eval=FALSE-------------------------------------------------- # res$BAM_matches ## ----------------------------------------------------------------------------- # [[1]] # [1] "DBW-40-1T" "DBW-40-2T" "DBW-40-3T" "DBW-43-N" # # [[2]] # [1] "DBW-40-2T" "DBW-40-3T" "DBW-43-N" # # [[3]] # [1] "DBW-40-3T" "DBW-43-N" # # [[4]] # [1] "DBW-40-N" "DBW-43-1T" ## ----cor, eval=FALSE---------------------------------------------------------- # cor_table = cor(res$AF_table) ## ----cortable, echo=FALSE----------------------------------------------------- cor_table = structure(c(1, 0.971671361359591, 0.982608032160979, 0.381966662753787, 0.380812832617918, 0.97246945978859, 0.971671361359591, 1, 0.988268712494756, 0.365843547670381, 0.364768267525972, 0.933880555972565, 0.982608032160979, 0.988268712494756, 1, 0.376165783421095, 0.375700923176265, 0.959717559987264, 0.381966662753787, 0.365843547670381, 0.376165783421095, 1, 0.979259788301874, 0.385257303482557, 0.380812832617918, 0.364768267525972, 0.375700923176265, 0.979259788301874, 1, 0.384975386482912, 0.97246945978859, 0.933880555972565, 0.959717559987264, 0.385257303482557, 0.384975386482912, 1), .Dim = c(6L, 6L), .Dimnames = list(c("DBW-40-1T", "DBW-40-2T", "DBW-40-3T", "DBW-40-N", "DBW-43-1T", "DBW-43-N"), c("DBW-40-1T", "DBW-40-2T", "DBW-40-3T", "DBW-40-N", "DBW-43-1T", "DBW-43-N"))) ## ----pheatmap2, fig.width=6, fig.height=4------------------------------------- pheatmap::pheatmap(cor_table, breaks = seq(0, 1, 0.01)) ## ----tcgaAvailable------------------------------------------------------------ tcga_avail = tcgaAvailable() head(tcga_avail, 3) ## ----tcgaLoad----------------------------------------------------------------- # By default MAF from MC3 project will be loaded laml_mc3 = tcgaLoad(study = "LAML") laml_mc3 # Change the source to Firehose laml_fh = tcgaLoad(study = "LAML", source = "Firehose") laml_fh ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install(pkgs = "PoisonAlien/TCGAmutations") ## ----maf2mae------------------------------------------------------------------ laml_mae = maf2mae(m = laml) laml_mae ## ----------------------------------------------------------------------------- sessionInfo()