# Allele-Specific Copy Number Analysis of Tumors

## Documentation for package ‘ASCAT’ version 3.2.0

- DESCRIPTION file.

## Help Pages

ascat.asmultipcf | Allele-specific segmentation of multiple samples
ascat.aspcf | ascat.aspcf
ascat.correctLogR | ascat.correctLogR
ascat.GCcorrect | ascat.GCcorrect
ascat.getAlleleCounts | Obtain allele counts for a given set of loci through external program alleleCounter.
ascat.getBAFsAndLogRs | Obtain BAF and LogR from the allele counts.
ascat.loadData | ascat.loadData
ascat.metrics | Function to extract different metrics from ASCAT profiles.
ascat.plotAdjustedAscatProfile | ascat.plotAdjustedAscatProfile
ascat.plotAscatProfile | ascat.plotAscatProfile
ascat.plotGenotypes | ascat.plotGenotypes
ascat.plotNonRounded | ascat.plotNonRounded
ascat.plotRawData | ascat.plotRawData
ascat.plotSegmentedData | ascat.plotSegmentedData
ascat.plotSunrise | ascat.plotSunrise
ascat.predictGermlineGenotypes | ascat.predictGermlineGenotypes
ascat.prepareHTS | Extract both logR and BAF values from sequencing data
ascat.prepareTargetedSeq | Method to extract a curated list of SNPs covered by a targeted sequencing experiment.
ascat.runAscat | ascat.runAscat
ascat.synchroniseFiles | Synchronise SNPs across files