Files in maftools

Summarize, Analyze and Visualize MAF Files

README.md

NAMESPACE

DESCRIPTION

LICENSE

R/compareSignatures.R R/rainfallPlot.R R/refineClusters.R R/prepareMutSig.R R/validateMaf.R R/print_mat.R R/estimate_binconf.R R/drugInteractions.R R/read_maf_dt.R R/mafSurvGroup.R R/plotTiTv.R R/clusterScore.R R/mafGeneSummary.R R/tmb.R R/plotClinicalEnrichment.R R/plotClusters.R R/lollipopPlot.R R/domainSummary.R R/oncomatrix.R R/somaticInteractions.R R/lollipopPlot2.R R/plotSignatures.R R/forestPlot.R R/extractSignatures.R R/mafObjects.R R/maf_methods.R R/plotApobecDiff.R R/addOncoprint.R R/plotOncodriveClust.R R/signatureCorrelation.R R/annovarToMaf.R R/titv.R R/subsetMaf.R R/gisticBubblePlot.R R/readGistic.R R/coOncoplot.R R/oncoPathway.R R/fisherCorrect.R R/inferTumHetero.R R/driverBP.R R/summarizeMaf.R R/repelPoints.R R/ClinicalEnrichment.R R/coBarplot.R R/get_lp_data.R R/mafSuvival.R R/mergeMafs.R R/genesToBarcodes.R R/icgc_to_maf.R R/oncoplot.R R/dashboard.R R/filterCopyNumber.R R/oncostrip.R R/plotPathways.R R/mathScore.R R/plotMafSummary.R R/plot_cbs_segs.R R/countMatrix.R R/tcgacompare.R R/gisticChromPlot.R R/mafCompare.R R/summarizeGistic.R R/writeGisticSummary.R R/gisticOncoPlot.R R/detect_kataegis.R R/plot_vaf.R R/setMaf.R R/snpMatrix.R R/wrteMafSummary.R R/gisticObject.R R/estimateSignatures.R R/plotCophenetic.R R/oncodrive.R R/vafComapre.R R/survGroup.R R/filterMaf.R R/readSegs.R R/TrinucleotideMatrix.R inst/NEWS.md

inst/CITATION

inst/old_news

inst/doc/oncoplots.R

inst/doc/oncoplots.html

inst/doc/maftools.html

inst/doc/oncoplots.Rmd inst/doc/maftools.Rmd inst/doc/maftools.R

inst/extdata/SBS_signatures.RDs

inst/extdata/amp_genes.conf_99.txt

inst/extdata/legacy_signatures.RDs

inst/extdata/all_lesions.conf_99.txt

inst/extdata/APL_primary.maf.gz

inst/extdata/tcga_cohort.txt.gz

inst/extdata/brca.maf.gz

inst/extdata/prot_len.txt.gz

inst/extdata/variants.hg19_multianno.txt

inst/extdata/hugo_to_mutSigSymbol.txt.gz

inst/extdata/tcga_laml_annot.tsv

inst/extdata/TCGA.AB.3009.hg19.seg.txt

inst/extdata/variants.tsv

inst/extdata/ensGenes.txt.gz

inst/extdata/drugs.tsv.gz

inst/extdata/oncogenic_sig_patwhays.tsv

inst/extdata/tcga_laml.maf.gz

inst/extdata/categories.tsv.gz

inst/extdata/LAML_sig_genes.txt.gz

inst/extdata/del_genes.conf_99.txt

inst/extdata/simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz

inst/extdata/APL_relapse.maf.gz

inst/extdata/pancan.txt.gz

inst/extdata/scores.gistic

inst/extdata/protein_domains.RDs

inst/extdata/BP_SMGs.txt.gz

build/vignette.rds

vignettes/corp-styles.css

vignettes/overview.png

vignettes/oncoplots.Rmd vignettes/maftools.Rmd

vignettes/maftools_hex.svg

vignettes/maftools.png

man/rainfallPlot.Rd man/plotmafSummary.Rd man/plotSignatures.Rd man/MAF-class.Rd man/plotCophenetic.Rd man/clinicalEnrichment.Rd man/plotCBSsegments.Rd man/mafSurvGroup.Rd man/icgcSimpleMutationToMAF.Rd man/drugInteractions.Rd man/somaticInteractions.Rd man/tcgaCompare.Rd man/oncodrive.Rd man/getGeneSummary.Rd man/oncostrip.Rd man/gisticBubblePlot.Rd man/lollipopPlot.Rd man/filterMaf.Rd man/vafCompare.Rd man/readGistic.Rd man/inferHeterogeneity.Rd man/write.GisticSummary.Rd man/annovarToMaf.Rd man/plotVaf.Rd man/gisticChromPlot.Rd man/coBarplot.Rd man/plotOncodrive.Rd man/plotTiTv.Rd man/survGroup.Rd man/titv.Rd man/estimateSignatures.Rd man/trinucleotideMatrix.Rd man/mafSummary.Rd man/setMaf.Rd man/tmb.Rd man/lollipopPlot2.Rd man/read.maf.Rd man/forestPlot.Rd man/PlotOncogenicPathways.Rd man/GISTIC-class.Rd man/compareSignatures.Rd man/math.score.Rd man/subsetMaf.Rd man/write.mafSummary.Rd man/plotEnrichmentResults.Rd man/coOncoplot.Rd man/OncogenicPathways.Rd man/prepareMutSig.Rd man/getFields.Rd man/genotypeMatrix.Rd man/mafSurvival.Rd man/getClinicalData.Rd man/plotApobecDiff.Rd man/getSampleSummary.Rd man/mafCompare.Rd man/extractSignatures.Rd man/tcgaDriverBP.Rd man/gisticOncoPlot.Rd man/oncoplot.Rd man/genesToBarcodes.Rd man/getCytobandSummary.Rd man/merge_mafs.Rd man/plotClusters.Rd man/mutCountMatrix.Rd man/pfamDomains.Rd man/signatureEnrichment.Rd scripts/estimate_tcga_tmb.R

maftools documentation built on Feb. 6, 2021, 2 a.m.