Class GISTIC
Class MAF
Construct an MAF object
Enrichment of known oncogenic pathways
Plot oncogenic pathways
Converts annovar annotations into MAF.
extract nucleotide counts for targeted variants from the BAM file.
Genotype known cancer hotspots from the tumor BAM file
Performs mutational enrichment analysis for a given clinical feature.
Draw two barplots side by side for cohort comparision.
Draw two oncoplots side by side for cohort comparision.
Compares identified denovo mutational signatures to known COSMIC signatures
Drug-Gene Interactions
Estimate number of signatures based on cophenetic correlation metric
Extract mutational signatures from trinucleotide context.
Filter MAF objects
Draw forest plot for differences betweeen cohorts.
Extracts Tumor Sample Barcodes where the given genes are mutated.
Creates a Genotype Matrix for every variant
extract annotations from MAF object
extract cytoband summary from GISTIC object
extract available fields from MAF object
extract gene summary from MAF or GISTIC object
extract sample summary from MAF or GISTIC object
Plot gistic results as a bubble plot
Plot gistic results along linearized chromosome
Plot gistic results.
Converts ICGC Simple Somatic Mutation format file to MAF
Clusters variants based on Variant Allele Frequencies (VAF).
Draws lollipop plot of amino acid changes on to Protein structure.
Compare two lollipop plots
Convert MAF to MultiAssayExperiment object
compare two cohorts (MAF).
Summary statistics of MAF
Performs survival analysis for a geneset
Performs survival analysis
Creates a bar plot
calculates MATH (Mutant-Allele Tumor Heterogeneity) score.
Merge multiple mafs into single MAF
Generates count matrix of mutations.
Detect cancer driver genes based on positional clustering of variants.
draw an oncoplot
draw an oncostrip similar to cBioportal oncoprinter output.
pfam domain annotation and summarization.
Plot differences between APOBEC enriched and non-APOBEC enriched samples.
Plots segmented copy number data.
Plot density plots from clutering results.
Draw an elbow plot of cophenetic correlation metric.
Plots results from clinicalEnrichment analysis
Plots results from 'oncodrive'
Display protein domains
Plots decomposed mutational signatures
Plot Transition and Trasnversion ratios.
Plots vaf distribution of genes
Plots maf summary.
Prepares MAF file for MutSig analysis.
Rainfall plot to display hyper mutated genomic regions.
Read MAF files.
Read and summarize gistic output.
Identify sample swaps and similarities
Set Operations for MAF objects
Performs sample stratification based on signature contribution and enrichment analysis.
Exact tests to detect mutually exclusive, co-occuring and altered genesets.
Subset MAF objects
Predict genesets associated with survival
Prints available TCGA datasets
Compare mutation load against TCGA cohorts
Compare genes to known TCGA drivers and their biological pathways
Loads a TCGA cohort
Classifies SNPs into transitions and transversions
Estimate Tumor Mutation Burden
Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores.
compare VAF across two cohorts
Writes GISTIC summaries to output tab-delimited text files.
Writes maf summaries to output tab-delimited text files.