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.
data(exomecounts)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.
link{RangedData}