Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.
|Date of publication||None|
|Maintainer||Michael Love <email@example.com>|
|License||GPL (>= 2)|
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...
ExomeCopy-class: Class "ExomeCopy"
exomeCopy-package: Copy number variant detection from exome sequencing read...
exomecounts: Sample counts from 16 exome sequencing samples from 1000...
generateBackground: Generate median background read depth
getGCcontent: Get the GC content of target ranges from a reference FASTA...
negLogLike: Generalized negative log likelihood and Viterbi algorithms
plotCompiledCNV: Plot compiled CNV segments for one sequence/chromosome
plot.exomeCopyObject: Plot function for exomeCopy
subdivideGRanges: Subdivide ranges of a GRanges object into nearly equal width...