Allele-Specific Copy Number Analysis of Tumors
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Documentation for package ‘ASCAT’ version 3.2.0
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 |