annovarToMaf | Converts annovar annotations into MAF. |
coOncoplot | Draw two oncoplots side by side for cohort comparision. |
extractSignatures | Extract mutational signatures from trinucletide context. |
forestPlot | Draw forest plot for differences betweeen cohorts. |
geneCloud | Plots wordcloud. |
genesToBarcodes | Extracts Tumor Sample Barcodes where the given genes are mutated. |
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 |
gisticPlot | Plot gistic results. |
icgcSimpleMutationToMAF | Converts ICGC Simple Somatic Mutation format file to MAF |
inferHeterogeneity | Clusters variants based on Variant Allele Frequencies (VAF). |
lollipopPlot | Draws lollipop plot of amino acid changes on to Protein structure. |
MAF | Class MAF |
MAF-class | Class MAF |
mafCompare | compare two cohorts (MAF). |
mafSurvival | Performs survival analysis |
math.score | calculates MATH (Mutant-Allele Tumor Heterogeneity) score. |
mutExclusive | Performs exact test for mutual exclusive events. |
oncodrive | Detect cancer driver genes based on positional clustering of variants. |
oncoplot | draw an oncoplot |
oncostrip | draw an oncostrip similar to cBioportal oncoprinter output. |
oncotate | Annotates given variants using oncotator api. |
pancanComparision | Perform PacCancer analysis |
pfamDomains | pfam domain annotation and summarization. |
plotCBSsegments | Plots segmented copy number data. |
plotClusters | Plot density plots from clutering results. |
plotGisticResults | Plot gistic results as a bubble plot or as a genomic segment plot. |
plotmafSummary | Plots maf summary. |
plotOncodrive | Plots results from 'oncodrive' |
plotSignatures | Plots decomposed mutational signatures or APOBEC enrichment plot. |
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. |
subsetMaf | Subset MAF |
tcgaCompare | Compare mutation load against TCGA cohorts |
titv | Classifies SNPs into transitions and transversions |
trinucleotideMatrix | Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores. |
vcr | Samll internal function to make complex events. |
write.GisticSummary | Writes GISTIC summaries to output tab-delimited text files. |
write.mafSummary | Writes maf summaries to output tab-delimited text files. |