maftools

Class GISTIC

Class MAF

Enrichment of known oncogenic pathways

Plot oncogenic pathways

Converts annovar annotations into MAF.

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

compare two cohorts (MAF).

Summary statistics of MAF

Performs survival analysis for a geneset

Performs survival analysis

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

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.

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

Compare mutation load against TCGA cohorts

Compare genes to known TCGA drivers and their biological pathways

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.