exomeCounts

This data set gives the read counts on chromosome 22 (hg19) 
of 22 samples in 3785 exons.  The rows correspond to targeted regions or exons 
and columns to samples.  An entry is the number of reads that map to the 
specific segment, i.e. targeted region or exon, of the sample. 
The GRanges object contains the information of the genomic location. The read 
counts were generated from freely available exome sequencing data of the 
1000Genomes Project.

datasets

cn.mops (Copy Number estimation by a Mixture Of PoissonS)
is a data processing pipeline for copy number variations and
aberrations (CNVs and CNAs) from next generation sequencing
(NGS) data. The package supplies functions to convert BAM files
into read count matrices or genomic ranges objects, which are
the input objects for cn.mops. cn.mops models the depths of
coverage across samples at each genomic position. Therefore, it
does not suffer from read count biases along chromosomes. Using
a Bayesian approach, cn.mops decomposes read variations across
samples into integer copy numbers and noise by its mixture
components and Poisson distributions, respectively. cn.mops
guarantees a low FDR because wrong detections are indicated by
high noise and filtered out. cn.mops is very fast and written
in C++.

Guenter Klambauer

cn.mops

cn.mops - Mixture of Poissons for CNV detection in NGS data

exomeCounts function

A GRanges object of 3785 rows and 22 columns.

Format

http://www.bioinf.jku.at/software/cnmops/cnmops.html.

exomeCounts: Read counts from exome sequencing for CNV detection

Description

Usage

Arguments

Format

Source

References