Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

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Documentation for package ‘superFreq’ version 1.4.2

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addBindingStrength Adds binding strength (essentailly same as GC content) to a bedfile.
analyse Analyse exomes
annotateQ Run VariantAnnotation on the provided variants
annotateSomaticQs Run VariantAnnotation on the provided samples
bamToPileup Gets pileup from bam over positions.
chrLengths The lengths of the chromsomes
chrToX convert chromsome and position to the single genomic coordinate x
cohortAnalyseBatch Analyse individuals for reccuring mutations
cohortAnalyseBatchContrast Analyse individuals for reccuring mutations
compareGroups Compares sets of individuals for reccuring mutations
defaultSuperParameters Returns default parameters
defaultSuperRuntimeSettings Returns default runtime settings
defaultSuperSettings Returns default settings
downloadTemplate Downloads resources and template for a standard analysis
dumpInput internal function for debugging purposes.
forceRedoEverything returns input that uses saved data if present.
forceRedoNothing returns input that uses saved data if present.
get104profile returns the 104 signature from a superFreq q variant object
getCohortMutationMatrix returns relevant mutations in samples in Genes of Interest
getCosmicCounts Retrieves information about cosmic variant IDs
getMoreVEPinfo Import more information about the variants
getSettings Wrapper for getting settings, containing defaults for missing values.
getStories Combines variants and CNAs to clonal evolution
getVariantsByIndividual Quality controls the variants in the vcfs, using the bams.
importCaptureRegions Imports capture regions from a bed file with GC information.
importSampleMetaData Imports metadata about the samples
loadData Loads saved data
makeFitPlots Plots results from differential coverage analysis
makeHeatmap plots a heatmap
makepHeatmap plots a heatmap
mcri Turns colours into similar colours from the Murdoch Childrens Research Institute palette.
mergeBatches Merges data from several batches for cohort analysis
moreVEPnames internal function
plotCNAheatmapOverGoI plots a heatmap of copy numbers, focusing on a gene of interest
plotCNAheatmapWithGoI plots a heatmap of copy numbers, highlighting genes of interest
plotCohortMutationHeatmap plots mutations in samples in Genes of Interest
plotColourScatter A better version of plot
plotCR plots a copy number profile
plotMA a plotting function for MA plots.
plotRiver plots a river plot
plotStories plots line plots of clonalities
postAnalyseVEP Runs VEP on a R and plot directory that superFreq has been run on.
printHTML generates an HTML to navigate superFreq output
qToGRanges Transforms a variant q data frame into granges
qualityScatter plots a scatter of the VAF between two samples
requireFileExists checks if a file exists, and creates an error if it doesnt.
runDE Run differential coverage analysis.
runSummaryPostAnalysis runs analyses across all samples in the batch
runVEP Run VEP on the provided variants
severityToType The variant effect as function of severity
shrug shruggie
superCohort looks for reccuring events across all individuals in a batch run
superFreq Wrapper to run default superFreq analysis
superInputFiles sets up and checks the input files for superFreq
superOutputDirectories Sets up and checks the output directories.
superVersion Return the current version of superFreq.
typeToSeverity Ranks the variant effects
VAconsequenceToSeverityRank coding' is used by the location run to cover all the coding variants, and will be replaced
vafScatter plots a scatter of the VAF between two samples
VAseverityToConsequence coding' is used by the location run to cover all the coding variants, and will be replaced
writeToVCF exports variants to VCF
xToChr Extract chromsome of genomic coordinate
xToGene find the gene closest to the genomic coordinate x
xToPos Extract position of genomic coordinate