R Graphical Manual

Last data update: 2014.03.03

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CranContrib
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Results 1 - 10 of 20 found.
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correctCoverageBias (Package: PureCN) : Correct for GC bias

Takes as input coverage data in GATK format (or data read by readCoverageGatk) and a mapping file for GC content, and then uses a loess normalization for bias correction. Largely follows the GC correction of the TitanCNA package.

● Data Source: BioConductor
● Keywords:
● Alias: correctCoverageBias
● 0 images

createCurationFile (Package: PureCN) : Create file to curate PureCN results

Function to create a CSV file that can be used to mark the correct solution in the output of a runAbsoluteCN() run.

● Data Source: BioConductor
● Keywords:
● Alias: createCurationFile
● 0 images

createExonWeightFile (Package: PureCN) : Calculate exon weights

Creates an exon weight file useful for segmentation. Requires a set of GATK coverage files from normal samples. A small number of tumor (or other normal) samples is then tested against all normals. Exon weights will be set proportional to the inverse of coverage standard deviation across all normals. Exons with high variance in coverage in the pool of normals are thus down-weighted.

● Data Source: BioConductor
● Keywords:
● Alias: createExonWeightFile
● 0 images

createNormalDatabase (Package: PureCN) : Create database of normal samples

Function to create a database of normal samples, used to find a good match for tumor copy number normalization.

● Data Source: BioConductor
● Keywords:
● Alias: createNormalDatabase
● 0 images

createSNPBlacklist (Package: PureCN) : Create SNP black list

Function to create a black list of germline SNPs with expected allelic fraction (AF) smaller than 0.5 in diploid genomes.

● Data Source: BioConductor
● Keywords:
● Alias: createSNPBlacklist
● 0 images

filterVcfBasic (Package: PureCN) : Basic VCF filter function

Function to remove artifacts and low confidence/quality variant calls.

● Data Source: BioConductor
● Keywords:
● Alias: filterVcfBasic
● 0 images

filterVcfMuTect (Package: PureCN) : Filter VCF MuTect

Function to remove artifacts and low confidence/quality calls from a MuTect generated VCF file.

● Data Source: BioConductor
● Keywords:
● Alias: filterVcfMuTect
● 0 images

findBestNormal (Package: PureCN) : Find best normal sample in database

Function to find the best matching normal for a provided tumor sample.

● Data Source: BioConductor
● Keywords:
● Alias: findBestNormal
● 0 images

findFocal (Package: PureCN) : Find focal amplifications

Function to find focal amplifications in segmented data. This is automatically called in runAbsoluteCN.

● Data Source: BioConductor
● Keywords:
● Alias: findFocal
● 3 images

getSexFromCoverage (Package: PureCN) : Get sample sex from coverage

This function determines the sex of a sample by the coverage ratio of chrX and chrY. Loss of chromosome Y (LOY) can result in a wrong female call.

● Data Source: BioConductor
● Keywords:
● Alias: getSexFromCoverage
● 0 images