Copy number variant detection from exome sequencing read depth


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Documentation for package ‘exomeCopy’ version 1.4.4

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exomeCopy-package Copy number variant detection from exome sequencing read depth
compileCopyCountSegments Compile segments across samples
copyCountSegments Segments of identical copy count from exomeCopy
countBamInGRanges Count reads from BAM file in genomic ranges
exomeCopy Fit the exomeCopy or exomeCopyVar model to the observed counts.
ExomeCopy-class Class "ExomeCopy"
exomecounts Sample counts from 16 exome sequencing samples from 1000 Genomes Project
generateBackground Generate median background read depth
getGCcontent Get the GC content of target ranges from a reference FASTA file
negLogLike Generalized negative log likelihood and Viterbi algorithms
plot-method Class "ExomeCopy"
plot.ExomeCopy Plot function for exomeCopy
plotCompiledCNV Plot compiled CNV segments for one sequence/chromosome
show-method Class "ExomeCopy"
subdivideGRanges Subdivide ranges of a GRanges object into nearly equal width ranges
viterbiPath Generalized negative log likelihood and Viterbi algorithms