annovarToMaf | Converts annovar annotations into MAF. |
bamreadcounts | extract nucleotide counts for targeted variants from the BAM file. |
cancerhotspots | Genotype known cancer hotspots from the tumor BAM file |
clinicalEnrichment | Performs mutational enrichment analysis for a given clinical feature. |
coBarplot | Draw two barplots side by side for cohort comparision. |
compareSignatures | Compares identified denovo mutational signatures to known COSMIC signatures |
coOncoplot | Draw two oncoplots side by side for cohort comparision. |
drugInteractions | Drug-Gene Interactions |
estimateSignatures | Estimate number of signatures based on cophenetic correlation metric |
extractSignatures | Extract mutational signatures from trinucleotide context. |
filterMaf | Filter MAF objects |
forestPlot | Draw forest plot for differences betweeen cohorts. |
genesToBarcodes | Extracts Tumor Sample Barcodes where the given genes are mutated. |
genotypeMatrix | Creates a Genotype Matrix for every variant |
getClinicalData | extract annotations from MAF object |
getClinicalData-method | extract annotations from MAF object |
getCytobandSummary | extract cytoband summary from GISTIC object |
getCytobandSummary-method | extract cytoband summary from GISTIC object |
getFields | extract available fields from MAF object |
getFields-method | extract available fields from MAF object |
getGeneSummary | extract gene summary from MAF or GISTIC object |
getGeneSummary-method | extract gene summary from MAF or GISTIC object |
getSampleSummary | extract sample summary from MAF or GISTIC object |
getSampleSummary-method | extract sample summary from MAF or GISTIC object |
GISTIC | Class GISTIC |
GISTIC-class | Class GISTIC |
gisticBubblePlot | Plot gistic results as a bubble plot |
gisticChromPlot | Plot gistic results along linearized chromosome |
gisticOncoPlot | Plot gistic results. |
icgcSimpleMutationToMAF | Converts ICGC Simple Somatic Mutation format file to MAF |
inferHeterogeneity | Clusters variants based on Variant Allele Frequencies (VAF). |
intersectMAF | Set Operations for MAF objects |
lollipopPlot | Draws lollipop plot of amino acid changes on to Protein structure. |
lollipopPlot2 | Compare two lollipop plots |
MAF | Construct an MAF object |
MAF-class | Class MAF |
maf2mae | Convert MAF to MultiAssayExperiment object |
mafbarplot | Creates a bar plot |
mafCompare | compare two cohorts (MAF). |
mafSummary | Summary statistics of MAF |
mafSurvGroup | Performs survival analysis for a geneset |
mafSurvival | Performs survival analysis |
math.score | calculates MATH (Mutant-Allele Tumor Heterogeneity) score. |
merge_mafs | Merge multiple mafs into single MAF |
mutCountMatrix | Generates count matrix of mutations. |
oncodrive | Detect cancer driver genes based on positional clustering of variants. |
OncogenicPathways | Enrichment of known oncogenic pathways |
oncoplot | draw an oncoplot |
oncostrip | draw an oncostrip similar to cBioportal oncoprinter output. |
pfamDomains | pfam domain annotation and summarization. |
plotApobecDiff | Plot differences between APOBEC enriched and non-APOBEC enriched samples. |
plotCBSsegments | Plots segmented copy number data. |
plotClusters | Plot density plots from clutering results. |
plotCophenetic | Draw an elbow plot of cophenetic correlation metric. |
plotEnrichmentResults | Plots results from clinicalEnrichment analysis |
plotmafSummary | Plots maf summary. |
plotOncodrive | Plots results from 'oncodrive' |
PlotOncogenicPathways | Plot oncogenic pathways |
plotProtein | Display protein domains |
plotSignatures | Plots decomposed mutational signatures |
plotTiTv | Plot Transition and Trasnversion ratios. |
plotVaf | Plots vaf distribution of genes |
prepareMutSig | Prepares MAF file for MutSig analysis. |
rainfallPlot | Rainfall plot to display hyper mutated genomic regions. |
read.maf | Read MAF files. |
readGistic | Read and summarize gistic output. |
sampleSwaps | Identify sample swaps and similarities |
setdiffMAF | Set Operations for MAF objects |
signatureEnrichment | Performs sample stratification based on signature contribution and enrichment analysis. |
somaticInteractions | Exact tests to detect mutually exclusive, co-occuring and altered genesets. |
subsetMaf | Subset MAF objects |
survGroup | Predict genesets associated with survival |
tcgaAvailable | Prints available TCGA datasets |
tcgaCompare | Compare mutation load against TCGA cohorts |
tcgaDriverBP | Compare genes to known TCGA drivers and their biological pathways |
tcgaLoad | Loads a TCGA cohort |
titv | Classifies SNPs into transitions and transversions |
tmb | Estimate Tumor Mutation Burden |
trinucleotideMatrix | Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores. |
vafCompare | compare VAF across two cohorts |
write.GisticSummary | Writes GISTIC summaries to output tab-delimited text files. |
write.mafSummary | Writes maf summaries to output tab-delimited text files. |