exomecounts: Sample counts from 16 exome sequencing samples from 1000...

In exomeCopy: Copy number variant detection from exome sequencing read depth

Description

This data set gives sample read counts in 1000 genomic ranges for 16 exome sequencing samples from the PUR population of the 1000 Genomes Project, along with the GC-content in the ranges. For instructions on how to prepare read count and covariate data, please see the example code in the man pages for subdivideGRanges and countBamInGRanges.

The genomic ranges are generated from small portion of the CCDS regions of chromosome 1 (hg19). The CCDS regions are subdivided evenly into ranges around 100bp using the subdivideGRanges function with default settings. Only ranges with positive counts across samples are retained. These regions were downloaded as a BED file from the UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway). The mapping files for the exome sequencing data and descriptions of the experiments are available at the 1000 Genomes Project website (http://www.1000genomes.org/data). The directories used are listed in the file 1000Genomes_files.txt in the extdata directory.

The column names are the sample names from the 1000 Genomes Project. Library format is paired-end reads and sample counts reflect both sequenced reads counted in their respective genomic ranges.

Usage

data(exomecounts)

Format

A GRanges object.

Source

1000 Genomes Project and Consensus Coding Sequence Project

References

1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010). http://dx.doi.org/10.1038/nature09534.

1000 Genomes Project: Release of phase 1 exome alignments http://www.1000genomes.org/announcements/release-phase-1-exome-alignments-2011-07-19

Pruitt, K. D. et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome research 19, 1316-1323 (2009). http://dx.doi.org/10.1101/gr.080531.108.

See Also

GRanges

exomeCopy documentation built on Nov. 8, 2020, 7:45 p.m.