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Object returned by exomeCopy
● Data Source:
BioConductor
● Keywords: classes
● Alias: ExomeCopy-class, plot,ExomeCopy,missing-method, show,ExomeCopy-method
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A short function which extracts the segments of constant copy count using the copyCountSegments function on a named list of named lists containing fitted ExomeCopy objects. See vignette for a full example of multiple samples and chromosomes.
● Data Source:
BioConductor
● Keywords:
● Alias: compileCopyCountSegments
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Unpacks an ExomeCopy object and returns a RangedData object with segments of identical predicted copy count in genomic coordinates.
● Data Source:
BioConductor
● Keywords:
● Alias: copyCountSegments
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Counts the number of reads with a specified minimum mapping quality from BAM files in genomic ranges specified by a GRanges object. This is a convenience function for counting the reads in ranges covering the targeted regions, such as the exons in exome enrichment experiments, from each sample. These read counts are used by exomeCopy in predicting CNVs in samples.
● Data Source:
BioConductor
● Keywords:
● Alias: countBamInGRanges
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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.
● Data Source:
BioConductor
● Keywords: package
● Alias: exomeCopy-package
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Fits a hidden Markov model to observed read counts using positional covariates. It returns an object containing the fitted parameters and the Viterbi path, the most likely path of hidden states, which is the predicted copy count at each window.
● Data Source:
BioConductor
● Keywords:
● Alias: exomeCopy
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Normalizes a set of columns representing read counts from different samples by their mean. Then calculates a statistic across the rows of normalized counts.
● Data Source:
BioConductor
● Keywords:
● Alias: generateBackground
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A short function using scanFa from the Rsamtools package on a target GRanges and a reference FASTA file
● Data Source:
BioConductor
● Keywords:
● Alias: getGCcontent
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negLogLike: Returns the negative log likelihood calculated with the forward equations.
● Data Source:
BioConductor
● Keywords:
● Alias: negLogLike, viterbiPath
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Plots the predicted copy count segments of an ExomeCopy object
● Data Source:
BioConductor
● Keywords:
● Alias: plot.ExomeCopy
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providing 
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