mm10.5kbp.SR50: Mm10 5kbp bin annotations

In tgac-vumc/QDNAseq.mm10: Bin annotation mm10

Description

Bin annotations are caclulated for non overlapping 5kbp bins generated as described in Scheinin et al. (see references). The annotated data frame contains:

• chromosome: Chromosome name,

• start: Base pair start position,

• end: Base pair end position,

• bases: Percentage of non-N nucleotides (of full bin size),

• gc: Percentage of C and G nucleotides (of non-N nucleotides),

• mappability: Average mappability of 50mers with a maximum of 2 mismatches as described in by Derrien et al. (see references),

• blacklist: Percent overlap with ENCODE blacklisted regions (unused, ENCODE blacklist data is not available for mouse),

• residual: Median loess residual calculated from normal C57BL/6J mouse samples from Gnerre et al. (see references),

• use: Whether the bin should be used in subsequent analysis steps,

Value

Returns an AnnotatedDataFrame object.

Author(s)

Daoud Sie

References

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Scheinin I, Sie D, Bengtsson H, van de Wiel M, Olshen A, van Thuijl H, van Essen H, Eijk P, Rustenburg F, Meijer G, Reijneveld J, Wesseling P, Pinkel D, Albertson D, Ylstra B 2014 Genome Research vol: 24 (12) pp: 1–11

Fast Computation and Applications of Genome Mappability. Derrien T, Estelle J, Sola S, Knowles D, Raineri E, Guigo R, Ribeca P January 19, 2012 PLOS ONE doi: 10.1371/journal.pone.0030377

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Gnerre S, Maccallum I, Przybylski D, Ribeiro F, Burton J, Walker B, Sharpe T, Hall G, Shea T, Sykes S, Berlin A, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander E, Jaffe D 2011 Proceedings of the National Academy of Sciences of the United States of America vol: 108 no. 4 1512–1518 doi: 10.1073/pnas.1017351108

Examples

data("mm10.5kbp.SR50")
assign("bins", get("mm10.5kbp.SR50"))
## Not run: readCounts <- binReadCounts(bins=bins, path="./bam")

# or

bins <- getBinAnnotations(binSize=5, genome="mm10")
## Not run: readCounts <- binReadCounts(bins=bins, path="./bam")

tgac-vumc/QDNAseq.mm10 documentation built on May 31, 2019, 9 a.m.